^SAMPLE=Stam_GM12872_CTCF_2nd
!Sample_title = Stam_GM12872_CTCF_2nd
!Sample_source_name = GM12872
!Sample_organism = Human
!Sample_characteristics = cell: GM12872
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: B-Lymphocyte
!Sample_characteristics = cell karyotype: CEPH/UTAH PEDIGREE 1459, Epstein-Barr Virus, Male
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:GM12872_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = 597e763180392d6cbecf5393a5bdc458
!Sample_supplementary_file_1 = wgEncodeUwChIPSeqAlignmentsRep2Gm12872Ctcf.tagAlign.gz
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!Sample_supplementary_file_build_1 = hg18
!Sample_supplementary_file_2 = wgEncodeUwChIPSeqHotspotsRep2Gm12872Ctcf.broadPeak.gz
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!Sample_supplementary_file_3 = wgEncodeUwChIPSeqRawSignalRep2Gm12872Ctcf.wig.gz
!Sample_supplementary_file_checksum_3 = b57a76d08cc3b48e10b662e18f23ff4c
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_SAEC_H3K4me3_1st
!Sample_title = Stam_SAEC_H3K4me3_1st
!Sample_source_name = SAEC
!Sample_organism = Human
!Sample_characteristics = cell: SAEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Small Airway Epithelial Cells
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:SAEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = e286be16a896d137c29b4bccb890291f
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_K562_H3K4me3_1st
!Sample_title = Stam_K562_H3K4me3_1st
!Sample_source_name = K562
!Sample_organism = Human
!Sample_characteristics = cell: K562
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: leukemia
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/K562_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = 4678b44a76b7e39053fd3a8d6440ae08
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_HMEC_CTCF_1st
!Sample_title = Stam_HMEC_CTCF_1st
!Sample_source_name = HMEC
!Sample_organism = Human
!Sample_characteristics = cell: HMEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Mammary Epithelial Cells
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/Broad_Histone:HMEC_Bernstein_protocol.pdf <Open_Chromatin:HMEC_Crawford_protocol.pdf UW_Stam:HMEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_SK-N-SH_RA_CTCF_1st
!Sample_title = Stam_SK-N-SH_RA_CTCF_1st
!Sample_source_name = SK-N-SH_RA
!Sample_organism = Human
!Sample_characteristics = cell: SK-N-SH_RA
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: neuroblastoma cell line differentiated w/ retinoic acid
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_SK-N-SH_RA_CTCF_2nd
!Sample_title = Stam_SK-N-SH_RA_CTCF_2nd
!Sample_source_name = SK-N-SH_RA
!Sample_organism = Human
!Sample_characteristics = cell: SK-N-SH_RA
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: neuroblastoma cell line differentiated w/ retinoic acid
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_SAEC_CTCF_2nd
!Sample_title = Stam_SAEC_CTCF_2nd
!Sample_source_name = SAEC
!Sample_organism = Human
!Sample_characteristics = cell: SAEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Small Airway Epithelial Cells
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:SAEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_HeLa-S3_H3K27me3_2nd
!Sample_title = Stam_HeLa-S3_H3K27me3_2nd
!Sample_source_name = HeLa-S3
!Sample_organism = Human
!Sample_characteristics = cell: HeLa-S3
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: cervical carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HeLa-S3_H3K4me3_2nd
!Sample_title = Stam_HeLa-S3_H3K4me3_2nd
!Sample_source_name = HeLa-S3
!Sample_organism = Human
!Sample_characteristics = cell: HeLa-S3
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: cervical carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HMEC_H3K27me3_1st
!Sample_title = Stam_HMEC_H3K27me3_1st
!Sample_source_name = HMEC
!Sample_organism = Human
!Sample_characteristics = cell: HMEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Mammary Epithelial Cells
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/Broad_Histone:HMEC_Bernstein_protocol.pdf <Open_Chromatin:HMEC_Crawford_protocol.pdf UW_Stam:HMEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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^SAMPLE=Stam_HeLa-S3_H3K36me3_2nd
!Sample_title = Stam_HeLa-S3_H3K36me3_2nd
!Sample_source_name = HeLa-S3
!Sample_organism = Human
!Sample_characteristics = cell: HeLa-S3
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: cervical carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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!Sample_library_source = genomic
!Sample_library_selection = ChIP
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^SAMPLE=Stam_GM12874_CTCF_2nd
!Sample_title = Stam_GM12874_CTCF_2nd
!Sample_source_name = GM12874
!Sample_organism = Human
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!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: B-Lymphocyte
!Sample_characteristics = cell karyotype: CEPH/UTAH PEDIGREE 1459, Epstein-Barr Virus, Male
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
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!Sample_molecule = genomic DNA
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^SAMPLE=Stam_GM12878_H3K36me3_2nd
!Sample_title = Stam_GM12878_H3K36me3_2nd
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!Sample_characteristics = cell organism: Human
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!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K36me3
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!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/GM12878_protocol.pdf
!Sample_molecule = genomic DNA
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^SAMPLE=Stam_SAEC_CTCF_1st
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!Sample_characteristics = cell organism: Human
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!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
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!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:SAEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_SAEC_H3K36me3_1st
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!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 1
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^SAMPLE=Stam_HRE_H3K27me3_2nd
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!Sample_characteristics = cell organism: Human
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!Sample_characteristics = cell sex: U
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_biomaterial_provider = Lonza
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!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_GM12878_H3K4me3_1st
!Sample_title = Stam_GM12878_H3K4me3_1st
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/GM12878_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_BJ_CTCF_1st
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!Sample_characteristics = cell organism: Human
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_biomaterial_provider = ATCC
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^SAMPLE=Stam_K562_H3K27me3_1st
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^SAMPLE=Stam_Caco-2_H3K27me3_2nd
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!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = e110a33a93d913e0f0693716fbe298e6
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!Sample_supplementary_file_checksum_3 = d26f5ba80af571da69f01a2dcd710355
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^SAMPLE=Stam_K562_CTCF_1st
!Sample_title = Stam_K562_CTCF_1st
!Sample_source_name = K562
!Sample_organism = Human
!Sample_characteristics = cell: K562
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: leukemia
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/K562_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep1K562Ctcf.fastq.gz
!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 22634242d2d2b8d6b0fde459ed09bcb6
!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = 754e00be0189645a7a4fcd1fb2d64ad5
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_NHEK_H3K36me3_2nd
!Sample_title = Stam_NHEK_H3K36me3_2nd
!Sample_source_name = NHEK
!Sample_organism = Human
!Sample_characteristics = cell: NHEK
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Normal Human Epidermal Keratinocytes
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/Keratinocyte_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 3c7621943ebba45d80aa986f1e552b9c
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_HRE_CTCF_1st
!Sample_title = Stam_HRE_CTCF_1st
!Sample_source_name = HRE
!Sample_organism = Human
!Sample_characteristics = cell: HRE
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Renal Epithelial cells (normal)
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:HRE_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep1HreCtcf.fastq.gz
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!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = caba070c77f1f8878b336a3a8aef88af
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_SAEC_H3K4me3_2nd
!Sample_title = Stam_SAEC_H3K4me3_2nd
!Sample_source_name = SAEC
!Sample_organism = Human
!Sample_characteristics = cell: SAEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Small Airway Epithelial Cells
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:SAEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_checksum_3 = 2ae291e77278a2fa71495adc223ed318
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_GM12872_CTCF_1st
!Sample_title = Stam_GM12872_CTCF_1st
!Sample_source_name = GM12872
!Sample_organism = Human
!Sample_characteristics = cell: GM12872
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: B-Lymphocyte
!Sample_characteristics = cell karyotype: CEPH/UTAH PEDIGREE 1459, Epstein-Barr Virus, Male
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:GM12872_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_K562_H3K36me3_1st
!Sample_title = Stam_K562_H3K36me3_1st
!Sample_source_name = K562
!Sample_organism = Human
!Sample_characteristics = cell: K562
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: leukemia
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/K562_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_BJ_H3K36me3_1st
!Sample_title = Stam_BJ_H3K36me3_1st
!Sample_source_name = BJ
!Sample_organism = Human
!Sample_characteristics = cell: BJ
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: skin fibroblast
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: "The line was established from skin taken from normal foreskin." - ATCC
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K36me3
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!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:BJ-tert_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HeLa-S3_CTCF_2nd
!Sample_title = Stam_HeLa-S3_CTCF_2nd
!Sample_source_name = HeLa-S3
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!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: cervical carcinoma
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!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_GM06990_H3K27me3_2nd
!Sample_title = Stam_GM06990_H3K27me3_2nd
!Sample_source_name = GM06990
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!Sample_characteristics = cell organism: Human
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!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_GM12865_CTCF_2nd
!Sample_title = Stam_GM12865_CTCF_2nd
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!Sample_characteristics = cell organism: Human
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!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
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!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
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!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_NHEK_H3K36me3_1st
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^SAMPLE=Stam_HeLa-S3_H3K36me3_1st
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!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf
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^SAMPLE=Stam_SK-N-SH_RA_H3K27me3_2nd
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^SAMPLE=Stam_HeLa-S3_H3K4me3_1st
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^SAMPLE=Stam_GM12878_CTCF_1st
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^SAMPLE=Stam_HRE_H3K4me3_1st
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^SAMPLE=Stam_GM12875_CTCF_2nd
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^SAMPLE=Stam_GM12878_H3K27me3_1st
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^SAMPLE=Stam_GM12801_CTCF_1st
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^SAMPLE=Stam_HepG2_H3K4me3_2nd
!Sample_title = Stam_HepG2_H3K4me3_2nd
!Sample_source_name = HepG2
!Sample_organism = Human
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!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: liver carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: endoderm
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
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!Sample_biomaterial_provider = ATCC
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!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_GM12864_CTCF_1st
!Sample_title = Stam_GM12864_CTCF_1st
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!Sample_characteristics = antibody: CTCF
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!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_HRE_H3K27me3_1st
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!Sample_source_name = HRE
!Sample_organism = Human
!Sample_characteristics = cell: HRE
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Renal Epithelial cells (normal)
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_molecule = genomic DNA
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^SAMPLE=Stam_HepG2_H3K27me3_1st
!Sample_title = Stam_HepG2_H3K27me3_1st
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!Sample_characteristics = antibody: H3K27me3
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_biomaterial_provider = ATCC
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^SAMPLE=Stam_NHEK_H3K4me3_2nd
!Sample_title = Stam_NHEK_H3K4me3_2nd
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!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
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!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
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!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_Caco-2_H3K4me3_1st
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_biomaterial_provider = ATCC
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!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_SAEC_H3K36me3_2nd
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!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K36me3
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!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
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!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_HEK293_CTCF_2nd
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!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
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^SAMPLE=Stam_HRE_H3K4me3_2nd
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^SAMPLE=Stam_NHEK_H3K27me3_2nd
!Sample_title = Stam_NHEK_H3K27me3_2nd
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!Sample_characteristics = cell lineage: ectoderm
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!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/Keratinocyte_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = bbc70481d269dfd0f7a6f7ea54f21623
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!Sample_supplementary_file_checksum_3 = 9942f025cf13d01e595ed5b29321688c
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_GM06990_H3K27me3_1st
!Sample_title = Stam_GM06990_H3K27me3_1st
!Sample_source_name = GM06990
!Sample_organism = Human
!Sample_characteristics = cell: GM06990
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: lymphoblastoid (CEPH)
!Sample_characteristics = cell karyotype: relatively normal
!Sample_characteristics = cell lineage: CEPH/Utah - European Caucasion; Epstein-Barr Virus
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_supplementary_file_checksum_4 = e5849bcaf9a7360ae706e16a2e8d4eca
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_BJ_H3K4me3_1st
!Sample_title = Stam_BJ_H3K4me3_1st
!Sample_source_name = BJ
!Sample_organism = Human
!Sample_characteristics = cell: BJ
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: skin fibroblast
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: "The line was established from skin taken from normal foreskin." - ATCC
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:BJ-tert_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HUVEC_CTCF_1st
!Sample_title = Stam_HUVEC_CTCF_1st
!Sample_source_name = HUVEC
!Sample_organism = Human
!Sample_characteristics = cell: HUVEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Umbilical Vein Endothelial Cell
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: mesoderm
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HUVEC_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HepG2_H3K36me3_1st
!Sample_title = Stam_HepG2_H3K36me3_1st
!Sample_source_name = HepG2
!Sample_organism = Human
!Sample_characteristics = cell: HepG2
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: liver carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: endoderm
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HepG2_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
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^SAMPLE=Stam_HEK293_CTCF_1st
!Sample_title = Stam_HEK293_CTCF_1st
!Sample_source_name = HEK293
!Sample_organism = Human
!Sample_characteristics = cell: HEK293
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: embryonic kidney
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: endoderm
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HeLa-S3_CTCF_1st
!Sample_title = Stam_HeLa-S3_CTCF_1st
!Sample_source_name = HeLa-S3
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!Sample_characteristics = cell: HeLa-S3
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: cervical carcinoma
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!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
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!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_HRE_H3K36me3_1st
!Sample_title = Stam_HRE_H3K36me3_1st
!Sample_source_name = HRE
!Sample_organism = Human
!Sample_characteristics = cell: HRE
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Renal Epithelial cells (normal)
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K36me3
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!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:HRE_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_GM12874_CTCF_1st
!Sample_title = Stam_GM12874_CTCF_1st
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!Sample_biomaterial_provider = Coriell
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!Sample_molecule = genomic DNA
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^SAMPLE=Stam_HUVEC_CTCF_2nd
!Sample_title = Stam_HUVEC_CTCF_2nd
!Sample_source_name = HUVEC
!Sample_organism = Human
!Sample_characteristics = cell: HUVEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Umbilical Vein Endothelial Cell
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!Sample_characteristics = cell lineage: mesoderm
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
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!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HUVEC_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_BJ_H3K4me3_2nd
!Sample_title = Stam_BJ_H3K4me3_2nd
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!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: skin fibroblast
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: "The line was established from skin taken from normal foreskin." - ATCC
!Sample_characteristics = cell sex: M
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_biomaterial_provider = ATCC
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!Sample_molecule = genomic DNA
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^SAMPLE=Stam_K562_H3K27me3_2nd
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!Sample_characteristics = antibody vendor name: Millipore
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^SAMPLE=Stam_K562_H3K36me3_2nd
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^SAMPLE=Stam_GM06990_CTCF_1st
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^SAMPLE=Stam_Caco-2_CTCF_1st
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^SAMPLE=Stam_HUVEC_H3K27me3_1st
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!Sample_characteristics = cell organism: Human
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!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: mesoderm
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HUVEC_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = 792af517ce09c816269eec46732bf193
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = d629288b0be6920384c4e37f4728605a
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!Sample_supplementary_file_checksum_4 = c11a77989d1f7a9a1b284468b6f51426
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^SAMPLE=Stam_HRE_CTCF_2nd
!Sample_title = Stam_HRE_CTCF_2nd
!Sample_source_name = HRE
!Sample_organism = Human
!Sample_characteristics = cell: HRE
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Renal Epithelial cells (normal)
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:HRE_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep2HreCtcf.fastq.gz
!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_1 = wgEncodeUwChIPSeqAlignmentsRep2HreCtcf.tagAlign.gz
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!Sample_supplementary_file_build_2 = hg18
!Sample_supplementary_file_3 = wgEncodeUwChIPSeqHotspotsRep2HreCtcf.broadPeak.gz
!Sample_supplementary_file_checksum_3 = acbc3209c26e081cf6df4949fbac4ca7
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_GM06990_H3K36me3_1st
!Sample_title = Stam_GM06990_H3K36me3_1st
!Sample_source_name = GM06990
!Sample_organism = Human
!Sample_characteristics = cell: GM06990
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: lymphoblastoid (CEPH)
!Sample_characteristics = cell karyotype: relatively normal
!Sample_characteristics = cell lineage: CEPH/Utah - European Caucasion; Epstein-Barr Virus
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HepG2_CTCF_2nd
!Sample_title = Stam_HepG2_CTCF_2nd
!Sample_source_name = HepG2
!Sample_organism = Human
!Sample_characteristics = cell: HepG2
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: liver carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: endoderm
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HepG2_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
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!Sample_supplementary_file_checksum_3 = 0354a54d67ce1315c03551e4b39bbccc
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^SAMPLE=Stam_HL-60_H3K4me3_2nd
!Sample_title = Stam_HL-60_H3K4me3_2nd
!Sample_source_name = HL-60
!Sample_organism = Human
!Sample_characteristics = cell: HL-60
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human promyelocytic leukemia cells
!Sample_characteristics = cell karyotype: cancer, female
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:HL-60_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_supplementary_file_checksum_3 = 13b5e55ea08f34fb4a8fb737e46b5cb5
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_HUVEC_H3K27me3_2nd
!Sample_title = Stam_HUVEC_H3K27me3_2nd
!Sample_source_name = HUVEC
!Sample_organism = Human
!Sample_characteristics = cell: HUVEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Umbilical Vein Endothelial Cell
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: mesoderm
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HUVEC_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_checksum_3 = 3029880b290087a5ff6b30be7871bda5
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_GM12873_CTCF_1st
!Sample_title = Stam_GM12873_CTCF_1st
!Sample_source_name = GM12873
!Sample_organism = Human
!Sample_characteristics = cell: GM12873
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: B-Lymphocyte
!Sample_characteristics = cell karyotype: CEPH/UTAH PEDIGREE 1459, Epstein-Barr Virus, Female
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:GM12873_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_SAEC_H3K27me3_1st
!Sample_title = Stam_SAEC_H3K27me3_1st
!Sample_source_name = SAEC
!Sample_organism = Human
!Sample_characteristics = cell: SAEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Small Airway Epithelial Cells
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:SAEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = ef2c6e919eabf2397a0f43aa572a8524
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_Caco-2_H3K36me3_2nd
!Sample_title = Stam_Caco-2_H3K36me3_2nd
!Sample_source_name = Caco-2
!Sample_organism = Human
!Sample_characteristics = cell: Caco-2
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: colorectal adenocarcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_checksum_3 = 40428c893429402bf53d7ed881b48d6d
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_BJ_H3K36me3_2nd
!Sample_title = Stam_BJ_H3K36me3_2nd
!Sample_source_name = BJ
!Sample_organism = Human
!Sample_characteristics = cell: BJ
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: skin fibroblast
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: "The line was established from skin taken from normal foreskin." - ATCC
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:BJ-tert_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
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!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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^SAMPLE=Stam_HRE_H3K36me3_2nd
!Sample_title = Stam_HRE_H3K36me3_2nd
!Sample_source_name = HRE
!Sample_organism = Human
!Sample_characteristics = cell: HRE
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Renal Epithelial cells (normal)
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:HRE_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
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^SAMPLE=Stam_SK-N-SH_RA_H3K27me3_1st
!Sample_title = Stam_SK-N-SH_RA_H3K27me3_1st
!Sample_source_name = SK-N-SH_RA
!Sample_organism = Human
!Sample_characteristics = cell: SK-N-SH_RA
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: neuroblastoma cell line differentiated w/ retinoic acid
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_HL-60_H3K4me3_1st
!Sample_title = Stam_HL-60_H3K4me3_1st
!Sample_source_name = HL-60
!Sample_organism = Human
!Sample_characteristics = cell: HL-60
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human promyelocytic leukemia cells
!Sample_characteristics = cell karyotype: cancer, female
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:HL-60_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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!Sample_library_source = genomic
!Sample_library_selection = ChIP
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^SAMPLE=Stam_K562_CTCF_2nd
!Sample_title = Stam_K562_CTCF_2nd
!Sample_source_name = K562
!Sample_organism = Human
!Sample_characteristics = cell: K562
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: leukemia
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/K562_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_BJ_CTCF_2nd
!Sample_title = Stam_BJ_CTCF_2nd
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!Sample_organism = Human
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!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: skin fibroblast
!Sample_characteristics = cell karyotype: normal
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!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
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!Sample_biomaterial_provider = ATCC
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!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_SK-N-SH_RA_H3K36me3_2nd
!Sample_title = Stam_SK-N-SH_RA_H3K36me3_2nd
!Sample_source_name = SK-N-SH_RA
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!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: neuroblastoma cell line differentiated w/ retinoic acid
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!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K36me3
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!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
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!Sample_molecule = genomic DNA
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^SAMPLE=Stam_HepG2_H3K27me3_2nd
!Sample_title = Stam_HepG2_H3K27me3_2nd
!Sample_source_name = HepG2
!Sample_organism = Human
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!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: liver carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: endoderm
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!Sample_characteristics = antibody: H3K27me3
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!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
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!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_HepG2_H3K4me3_1st
!Sample_title = Stam_HepG2_H3K4me3_1st
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!Sample_organism = Human
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!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
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!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
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^SAMPLE=Stam_BJ_H3K27me3_1st
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!Sample_biomaterial_provider = ATCC
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^SAMPLE=Stam_SK-N-SH_RA_H3K36me3_1st
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^SAMPLE=Stam_HeLa-S3_H3K27me3_1st
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!Sample_characteristics = antibody vendor name: Millipore
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!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf
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^SAMPLE=Stam_GM12873_CTCF_2nd
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^SAMPLE=Stam_GM12878_H3K27me3_2nd
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^SAMPLE=Stam_HUVEC_H3K36me3_1st
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^SAMPLE=Stam_WERI-Rb-1_CTCF_1st
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^SAMPLE=Stam_NHEK_H3K27me3_1st
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^SAMPLE=Stam_HUVEC_H3K4me3_2nd
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^SAMPLE=Stam_GM12865_CTCF_1st
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!Sample_characteristics = cell: HUVEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Umbilical Vein Endothelial Cell
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: mesoderm
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HUVEC_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep1HuvecH3k4me3.fastq.gz
!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = d1856040790e4c791950ae3b58e88a25
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!Sample_supplementary_file_checksum_1 = 550692ba967c4b09e28be06bc1d71839
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!Sample_supplementary_file_checksum_3 = 34215698a8592f3802af0457f87cd8ea
!Sample_supplementary_file_build_3 = hg18
!Sample_supplementary_file_4 = wgEncodeUwChIPSeqRawSignalRep1HuvecH3k4me3.wig.gz
!Sample_supplementary_file_checksum_4 = e6d0675bcaf1b767672b75eb6a54eba5
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_NHEK_CTCF_1st
!Sample_title = Stam_NHEK_CTCF_1st
!Sample_source_name = NHEK
!Sample_organism = Human
!Sample_characteristics = cell: NHEK
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Normal Human Epidermal Keratinocytes
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/Keratinocyte_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep1NhekCtcf.fastq.gz
!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_1 = wgEncodeUwChIPSeqAlignmentsRep1NhekCtcf.tagAlign.gz
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 67e21a4006642f095c8b2b509722fb93
!Sample_supplementary_file_build_3 = hg18
!Sample_supplementary_file_4 = wgEncodeUwChIPSeqPeaksRep1NhekCtcf.narrowPeak.gz
!Sample_supplementary_file_checksum_4 = 3e0304793d3015819b2ed5a720c0bef3
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_Caco-2_H3K36me3_1st
!Sample_title = Stam_Caco-2_H3K36me3_1st
!Sample_source_name = Caco-2
!Sample_organism = Human
!Sample_characteristics = cell: Caco-2
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: colorectal adenocarcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep1Caco2H3k36me3.fastq.gz
!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = 37207cced7f23dee97e517c490aaed46
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_4 = b4b277ae1e06d752e732149d6a3f1f13
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_GM12875_CTCF_1st
!Sample_title = Stam_GM12875_CTCF_1st
!Sample_source_name = GM12875
!Sample_organism = Human
!Sample_characteristics = cell: GM12875
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: B-Lymphocyte
!Sample_characteristics = cell karyotype: CEPH/UTAH PEDIGREE 1459, Epstein-Barr Virus, Female
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:GM12875_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = 8ead3eb7c4c133192137d96ff4961a9f
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_GM12878_CTCF_2nd
!Sample_title = Stam_GM12878_CTCF_2nd
!Sample_source_name = GM12878
!Sample_organism = Human
!Sample_characteristics = cell: GM12878
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: lymphoblastoid
!Sample_characteristics = cell karyotype: relatively normal
!Sample_characteristics = cell lineage: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/GM12878_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep2Gm12878Ctcf.fastq.gz
!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_checksum_2 = 0cc106ffff56dcfddc741a841769775f
!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 7f45de1a7bef61c26f4ce6873e706375
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_GM06990_CTCF_2nd
!Sample_title = Stam_GM06990_CTCF_2nd
!Sample_source_name = GM06990
!Sample_organism = Human
!Sample_characteristics = cell: GM06990
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: lymphoblastoid (CEPH)
!Sample_characteristics = cell karyotype: relatively normal
!Sample_characteristics = cell lineage: CEPH/Utah - European Caucasion; Epstein-Barr Virus
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep2Gm06990Ctcf.fastq.gz
!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = 8e564f4d9e2d78fdaa134bf0f31c482b
!Sample_supplementary_file_1 = wgEncodeUwChIPSeqRawSignalRep2Gm06990Ctcf.wig.gz
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 676b05bcc02d6bcb581bb046a2009fda
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_BJ_H3K27me3_2nd
!Sample_title = Stam_BJ_H3K27me3_2nd
!Sample_source_name = BJ
!Sample_organism = Human
!Sample_characteristics = cell: BJ
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: skin fibroblast
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: "The line was established from skin taken from normal foreskin." - ATCC
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:BJ-tert_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 3ed30f593aa12a691dade60d7b212dab
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_NHEK_H3K4me3_1st
!Sample_title = Stam_NHEK_H3K4me3_1st
!Sample_source_name = NHEK
!Sample_organism = Human
!Sample_characteristics = cell: NHEK
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Normal Human Epidermal Keratinocytes
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/Keratinocyte_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_GM12878_H3K4me3_2nd
!Sample_title = Stam_GM12878_H3K4me3_2nd
!Sample_source_name = GM12878
!Sample_organism = Human
!Sample_characteristics = cell: GM12878
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: lymphoblastoid
!Sample_characteristics = cell karyotype: relatively normal
!Sample_characteristics = cell lineage: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/GM12878_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_GM06990_H3K4me3_2nd
!Sample_title = Stam_GM06990_H3K4me3_2nd
!Sample_source_name = GM06990
!Sample_organism = Human
!Sample_characteristics = cell: GM06990
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: lymphoblastoid (CEPH)
!Sample_characteristics = cell karyotype: relatively normal
!Sample_characteristics = cell lineage: CEPH/Utah - European Caucasion; Epstein-Barr Virus
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_supplementary_file_build_1 = hg18
!Sample_supplementary_file_2 = wgEncodeUwChIPSeqAlignmentsRep2Gm06990H3k4me3.tagAlign.gz
!Sample_supplementary_file_checksum_2 = f080c513c2b1db2bc2c58dff874ecdd3
!Sample_supplementary_file_build_2 = hg18
!Sample_supplementary_file_3 = wgEncodeUwChIPSeqHotspotsRep2Gm06990H3k4me3.broadPeak.gz
!Sample_supplementary_file_checksum_3 = bba46f6a65a832824620e383c5c4a108
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_HUVEC_H3K36me3_2nd
!Sample_title = Stam_HUVEC_H3K36me3_2nd
!Sample_source_name = HUVEC
!Sample_organism = Human
!Sample_characteristics = cell: HUVEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human Umbilical Vein Endothelial Cell
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: mesoderm
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HUVEC_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_checksum_1 = c20c05ba34f6704c5401a9c17efb093c
!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_checksum_2 = b55d1f5c3e0d59615a6358d059ac1568
!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = f0dd1efcf8cd5277cd692b21303f4f4c
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_NHEK_CTCF_2nd
!Sample_title = Stam_NHEK_CTCF_2nd
!Sample_source_name = NHEK
!Sample_organism = Human
!Sample_characteristics = cell: NHEK
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Normal Human Epidermal Keratinocytes
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell lineage: ectoderm
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/Keratinocyte_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep2NhekCtcf.fastq.gz
!Sample_raw_file_type_1 = fastq
!Sample_raw_file_checksum_1 = bf557b551202608ad9b016cc9370d401
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!Sample_supplementary_file_checksum_1 = 55f73699264a6b578ccd0f4d72819d2b
!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_checksum_2 = ac62a6f0a70e213dadad77fa56adaf76
!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = d966f178b1690640237d491b8fe42a99
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^SAMPLE=Stam_GM12864_CTCF_2nd
!Sample_title = Stam_GM12864_CTCF_2nd
!Sample_source_name = GM12864
!Sample_organism = Human
!Sample_characteristics = cell: GM12864
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: B-Lymphocyte
!Sample_characteristics = cell karyotype: CEPH/UTAH PEDIGREE 1459, Epstein-Barr Virus, Male
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:GM12864_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_checksum_3 = 51f30393509a9ba46f8dc63c10c56aef
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_Caco-2_H3K4me3_2nd
!Sample_title = Stam_Caco-2_H3K4me3_2nd
!Sample_source_name = Caco-2
!Sample_organism = Human
!Sample_characteristics = cell: Caco-2
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: colorectal adenocarcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: H3K4me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_checksum_2 = 139425ba186693f051a58a68c69d86f3
!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = e15a8a88a19d3412418680fc936a54d0
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_SAEC_H3K27me3_2nd
!Sample_title = Stam_SAEC_H3K27me3_2nd
!Sample_source_name = SAEC
!Sample_organism = Human
!Sample_characteristics = cell: SAEC
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Small Airway Epithelial Cells
!Sample_characteristics = cell karyotype: normal
!Sample_characteristics = cell sex: U
!Sample_characteristics = antibody: H3K27me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Lonza
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:SAEC_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 8738bdf8f8293c0a7e095cb56e0b29fd
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_GM06990_H3K36me3_2nd
!Sample_title = Stam_GM06990_H3K36me3_2nd
!Sample_source_name = GM06990
!Sample_organism = Human
!Sample_characteristics = cell: GM06990
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: lymphoblastoid (CEPH)
!Sample_characteristics = cell karyotype: relatively normal
!Sample_characteristics = cell lineage: CEPH/Utah - European Caucasion; Epstein-Barr Virus
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: H3K36me3
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.
!Sample_characteristics = antibody vendor name: Abcam
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = Coriell
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
!Sample_raw_file_1 = wgEncodeUwChIPSeqRawDataRep2Gm06990H3k36me3.fastq.gz
!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 827d1fe032dcce65f8e7d80fca23e23b
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_HepG2_CTCF_1st
!Sample_title = Stam_HepG2_CTCF_1st
!Sample_source_name = HepG2
!Sample_organism = Human
!Sample_characteristics = cell: HepG2
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: liver carcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell lineage: endoderm
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/HepG2_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = aa86a4c5c97210712a49abef6651b300
!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = d891a3e18a52e6ea90c0a6ba58a59b9b
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_HL-60_CTCF_1st
!Sample_title = Stam_HL-60_CTCF_1st
!Sample_source_name = HL-60
!Sample_organism = Human
!Sample_characteristics = cell: HL-60
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: Human promyelocytic leukemia cells
!Sample_characteristics = cell karyotype: cancer, female
!Sample_characteristics = cell sex: F
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 1
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:HL-60_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_2 = hg18
!Sample_supplementary_file_3 = wgEncodeUwChIPSeqRawSignalRep1Hl60Ctcf.wig.gz
!Sample_supplementary_file_checksum_3 = 7d289213939dd63f298926e02a4d28bd
!Sample_supplementary_file_build_3 = hg18
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!Sample_supplementary_file_checksum_4 = ebbed3b00a83ff70dfa587db371d0355
!Sample_supplementary_file_build_4 = hg18
^SAMPLE=Stam_Caco-2_CTCF_2nd
!Sample_title = Stam_Caco-2_CTCF_2nd
!Sample_source_name = Caco-2
!Sample_organism = Human
!Sample_characteristics = cell: Caco-2
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: colorectal adenocarcinoma
!Sample_characteristics = cell karyotype: cancer
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:Stam_15_protocols.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_raw_file_type_1 = fastq
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!Sample_supplementary_file_build_1 = hg18
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!Sample_supplementary_file_build_2 = hg18
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!Sample_supplementary_file_checksum_3 = 60415ad405fa0d7c386fbc1e245d3715
!Sample_supplementary_file_build_3 = hg18
^SAMPLE=Stam_WERI-Rb-1_CTCF_2nd
!Sample_title = Stam_WERI-Rb-1_CTCF_2nd
!Sample_source_name = WERI-Rb-1
!Sample_organism = Human
!Sample_characteristics = cell: WERI-Rb-1
!Sample_characteristics = cell organism: Human
!Sample_characteristics = cell description: retinoblastoma
!Sample_characteristics = cell sex: M
!Sample_characteristics = antibody: CTCF
!Sample_characteristics = antibody description: rabbit polyclonal
!Sample_characteristics = antibody target description: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
!Sample_characteristics = antibody vendor name: Millipore
!Sample_characteristics = replicate: 2
!Sample_biomaterial_provider = ATCC
!Sample_growth_protocol = Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/UW_Stam:WERI-Rb-1_Stam_protocol.pdf
!Sample_molecule = genomic DNA
!Sample_extract_protocol = For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_data_processing = For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Sample_library_strategy = ChIP-Seq
!Sample_library_source = genomic
!Sample_library_selection = ChIP
!Sample_instrument_model = Illumina Genome Analyzer
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!Sample_supplementary_file_build_3 = hg18
^SERIES=wgEncodeUwChIPSeq
!Series_title = ENCODE ChIP-seq by Univ. Washington
!Series_summary = This dataset is produced as part of the ENCODE Project and displays maps of histone modifications genome-wide in different cell lines, using ChIP-seq high-throughput sequencing.
!Series_summary = For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
!Series_overall_design = Cells were grown according to the approved ENCODE cell culture protocols. Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibody at 4 degrees C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligated to Illumina adapters and made in to Solexa library for sequencing. The sequencing reads uniquely mapping to the hg18 reference human genome were then scored using a scan statistic based on the binomial distribution. Regions of significant tag enrichment (significance being gauged using an FDR procedure based on randomly generated data) were then resolved into 150 bp peaks called on a continuous, sliding window tag density representation of the data (Sabo et al., 2004). Data were verified by sequencing biological replicates displaying correlation coefficient >0.9.
!Series_contributor = J,A,Stamatoyannopoulos
!Series_web_link = http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeUwChIPSeq
!Series_web_link = http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
!Series_sample_id = Stam_GM12872_CTCF_2nd
!Series_sample_id = Stam_SAEC_H3K4me3_1st
!Series_sample_id = Stam_K562_H3K4me3_1st
!Series_sample_id = Stam_HMEC_CTCF_1st
!Series_sample_id = Stam_SK-N-SH_RA_CTCF_1st
!Series_sample_id = Stam_SK-N-SH_RA_CTCF_2nd
!Series_sample_id = Stam_SAEC_CTCF_2nd
!Series_sample_id = Stam_HeLa-S3_H3K27me3_2nd
!Series_sample_id = Stam_HeLa-S3_H3K4me3_2nd
!Series_sample_id = Stam_HMEC_H3K27me3_1st
!Series_sample_id = Stam_HeLa-S3_H3K36me3_2nd
!Series_sample_id = Stam_GM12874_CTCF_2nd
!Series_sample_id = Stam_GM12878_H3K36me3_2nd
!Series_sample_id = Stam_SAEC_CTCF_1st
!Series_sample_id = Stam_SAEC_H3K36me3_1st
!Series_sample_id = Stam_HRE_H3K27me3_2nd
!Series_sample_id = Stam_GM12878_H3K4me3_1st
!Series_sample_id = Stam_BJ_CTCF_1st
!Series_sample_id = Stam_K562_H3K27me3_1st
!Series_sample_id = Stam_Caco-2_H3K27me3_2nd
!Series_sample_id = Stam_K562_CTCF_1st
!Series_sample_id = Stam_NHEK_H3K36me3_2nd
!Series_sample_id = Stam_HRE_CTCF_1st
!Series_sample_id = Stam_SAEC_H3K4me3_2nd
!Series_sample_id = Stam_GM12872_CTCF_1st
!Series_sample_id = Stam_K562_H3K36me3_1st
!Series_sample_id = Stam_BJ_H3K36me3_1st
!Series_sample_id = Stam_HeLa-S3_CTCF_2nd
!Series_sample_id = Stam_GM06990_H3K27me3_2nd
!Series_sample_id = Stam_GM12865_CTCF_2nd
!Series_sample_id = Stam_NHEK_H3K36me3_1st
!Series_sample_id = Stam_HeLa-S3_H3K36me3_1st
!Series_sample_id = Stam_SK-N-SH_RA_H3K27me3_2nd
!Series_sample_id = Stam_HeLa-S3_H3K4me3_1st
!Series_sample_id = Stam_GM12878_CTCF_1st
!Series_sample_id = Stam_HRE_H3K4me3_1st
!Series_sample_id = Stam_GM12875_CTCF_2nd
!Series_sample_id = Stam_GM12878_H3K27me3_1st
!Series_sample_id = Stam_GM12801_CTCF_1st
!Series_sample_id = Stam_HepG2_H3K4me3_2nd
!Series_sample_id = Stam_GM12864_CTCF_1st
!Series_sample_id = Stam_HRE_H3K27me3_1st
!Series_sample_id = Stam_HepG2_H3K27me3_1st
!Series_sample_id = Stam_NHEK_H3K4me3_2nd
!Series_sample_id = Stam_Caco-2_H3K4me3_1st
!Series_sample_id = Stam_SAEC_H3K36me3_2nd
!Series_sample_id = Stam_HEK293_CTCF_2nd
!Series_sample_id = Stam_HRE_H3K4me3_2nd
!Series_sample_id = Stam_NHEK_H3K27me3_2nd
!Series_sample_id = Stam_GM06990_H3K27me3_1st
!Series_sample_id = Stam_BJ_H3K4me3_1st
!Series_sample_id = Stam_HUVEC_CTCF_1st
!Series_sample_id = Stam_HepG2_H3K36me3_1st
!Series_sample_id = Stam_HEK293_CTCF_1st
!Series_sample_id = Stam_HeLa-S3_CTCF_1st
!Series_sample_id = Stam_HRE_H3K36me3_1st
!Series_sample_id = Stam_GM12874_CTCF_1st
!Series_sample_id = Stam_HUVEC_CTCF_2nd
!Series_sample_id = Stam_BJ_H3K4me3_2nd
!Series_sample_id = Stam_K562_H3K27me3_2nd
!Series_sample_id = Stam_K562_H3K36me3_2nd
!Series_sample_id = Stam_GM06990_CTCF_1st
!Series_sample_id = Stam_Caco-2_CTCF_1st
!Series_sample_id = Stam_GM06990_H3K4me3_1st
!Series_sample_id = Stam_Caco-2_H3K27me3_1st
!Series_sample_id = Stam_SK-N-SH_RA_H3K4me3_1st
!Series_sample_id = Stam_SK-N-SH_RA_H3K4me3_2nd
!Series_sample_id = Stam_HUVEC_H3K27me3_1st
!Series_sample_id = Stam_HRE_CTCF_2nd
!Series_sample_id = Stam_GM06990_H3K36me3_1st
!Series_sample_id = Stam_HepG2_CTCF_2nd
!Series_sample_id = Stam_HL-60_H3K4me3_2nd
!Series_sample_id = Stam_HUVEC_H3K27me3_2nd
!Series_sample_id = Stam_GM12873_CTCF_1st
!Series_sample_id = Stam_SAEC_H3K27me3_1st
!Series_sample_id = Stam_Caco-2_H3K36me3_2nd
!Series_sample_id = Stam_BJ_H3K36me3_2nd
!Series_sample_id = Stam_HRE_H3K36me3_2nd
!Series_sample_id = Stam_SK-N-SH_RA_H3K27me3_1st
!Series_sample_id = Stam_HL-60_H3K4me3_1st
!Series_sample_id = Stam_K562_CTCF_2nd
!Series_sample_id = Stam_BJ_CTCF_2nd
!Series_sample_id = Stam_SK-N-SH_RA_H3K36me3_2nd
!Series_sample_id = Stam_HepG2_H3K27me3_2nd
!Series_sample_id = Stam_HepG2_H3K4me3_1st
!Series_sample_id = Stam_BJ_H3K27me3_1st
!Series_sample_id = Stam_SK-N-SH_RA_H3K36me3_1st
!Series_sample_id = Stam_HeLa-S3_H3K27me3_1st
!Series_sample_id = Stam_GM12873_CTCF_2nd
!Series_sample_id = Stam_GM12878_H3K27me3_2nd
!Series_sample_id = Stam_HUVEC_H3K36me3_1st
!Series_sample_id = Stam_GM12878_H3K36me3_1st
!Series_sample_id = Stam_WERI-Rb-1_CTCF_1st
!Series_sample_id = Stam_NHEK_H3K27me3_1st
!Series_sample_id = Stam_HUVEC_H3K4me3_2nd
!Series_sample_id = Stam_GM12865_CTCF_1st
!Series_sample_id = Stam_HUVEC_H3K4me3_1st
!Series_sample_id = Stam_NHEK_CTCF_1st
!Series_sample_id = Stam_Caco-2_H3K36me3_1st
!Series_sample_id = Stam_GM12875_CTCF_1st
!Series_sample_id = Stam_GM12878_CTCF_2nd
!Series_sample_id = Stam_GM06990_CTCF_2nd
!Series_sample_id = Stam_BJ_H3K27me3_2nd
!Series_sample_id = Stam_NHEK_H3K4me3_1st
!Series_sample_id = Stam_GM12878_H3K4me3_2nd
!Series_sample_id = Stam_GM06990_H3K4me3_2nd
!Series_sample_id = Stam_HUVEC_H3K36me3_2nd
!Series_sample_id = Stam_NHEK_CTCF_2nd
!Series_sample_id = Stam_GM12864_CTCF_2nd
!Series_sample_id = Stam_Caco-2_H3K4me3_2nd
!Series_sample_id = Stam_SAEC_H3K27me3_2nd
!Series_sample_id = Stam_GM06990_H3K36me3_2nd
!Series_sample_id = Stam_HepG2_CTCF_1st
!Series_sample_id = Stam_HL-60_CTCF_1st
!Series_sample_id = Stam_Caco-2_CTCF_2nd
!Series_sample_id = Stam_WERI-Rb-1_CTCF_2nd