This directory contains Primer data for this ENCODE composite.

Primer data files include the sequences of the primers used in the
experiments. 

The 44 ENCODE regions were analyzed in two groups using two separate 5C primer
pools. The first group (ENm) contained the manually picked ENCODE regions,
ENm001-014 and ENr313. The second group (ENr) contained the 30 randomly picked
ENCODE regions.

ENm Primers: wgEncodeUmassDekker5CEnmPrimer.doc.tgz 

The primer pool for the ENm group contained a total of 3,150 primers (476
reverse 5C primers and 2674 forward 5C primers). This primer pool allows
interrogation of a total of 1,272,824 interactions. Of these, 83,427
interactions were between fragments that were both located in the same ENCODE
region.

ENr Primers: wgEncodeUmassDekker5CEnrPrimer.doc.tgz

The primer pool for the ENr group contained a total of 3,152 primers (505
reverse 5C primers and 2647 forward 5C primers). This primer pool allows
interrogation of a total of 1,336,735 interactions. Of these, 34,859
interactions were between fragments that were both located in the same ENCODE
region.

In total, 981 reverse primers and 5,321 forward primers were designed
(corresponding to ~77.1% (6,302/8,174) of all HindIII fragments in the 44
ENCODE regions).