Table 2.
ENCODE data sets and cell lines used for analysis: ChIP-Seq data for RNA Polymerase II (RNAPII), CTCF and various Histone marks, data for DNase I hypersensitive sites (DNase-Seq), methylation data from reduced representation bisulfite sequencing (methyl-RRBS) and sequencing of long polyA+ whole cell RNA (RNA-Seq). For HMEC and HSMM cells RNAPII ChIP-Seq data was not available at the time of our analyses. Datasets were generated at the Broad Institute (BROAD), Cold Spring Harbor Laboratory (CSHL), University of Washington (UW), University of Texas at Austin (UT-A), and Hudson Alpha (HA).
| Factor/mark | Pair 1 | Pair 2 | ||
|---|---|---|---|---|
| Cell lines | Cell lines | |||
| K562 | GM12878 | HSMM | HMEC | |
| CTCF | BROAD | BROAD | BROAD | BROAD |
| H3K27ac | BROAD | BROAD | BROAD | BROAD |
| H3K27me3 | BROAD | BROAD | BROAD | BROAD |
| H3K36me3 | BROAD | BROAD | BROAD | BROAD |
| H3K4me1 | BROAD | BROAD | BROAD | BROAD |
| H3K4me2 | BROAD | BROAD | BROAD | BROAD |
| H3K4me3 | BROAD | BROAD | BROAD | BROAD |
| H3K9ac | BROAD | BROAD | BROAD | BROAD |
| H4K20me1 | BROAD | BROAD | BROAD | BROAD |
| RNAPII | UT-A | UT-A | — | — |
| DNase-Seq | UW | UW | UW | UW |
| Methyl-RRBS | HA | HA | HA | HA |
| RNA-Seq | CSHL | CSHL | CSHL | CSHL |