International Journal of Genomics / 2012 / Article / Tab 2

Research Article

Predictive Models of Gene Regulation from High-Throughput Epigenomics Data

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/markPair 1Pair 2
Cell linesCell lines
K562GM12878HSMMHMEC

CTCFBROADBROADBROADBROAD
H3K27acBROADBROADBROADBROAD
H3K27me3BROADBROAD BROADBROAD
H3K36me3BROADBROADBROADBROAD
H3K4me1BROADBROADBROADBROAD
H3K4me2BROADBROADBROADBROAD
H3K4me3BROADBROADBROADBROAD
H3K9acBROADBROADBROADBROAD
H4K20me1BROADBROAD BROADBROAD
RNAPIIUT-AUT-A
DNase-SeqUWUWUWUW
Methyl-RRBSHAHAHAHA
RNA-Seq CSHLCSHLCSHLCSHL

We are committed to sharing findings related to COVID-19 as quickly as possible. We will be providing unlimited waivers of publication charges for accepted research articles as well as case reports and case series related to COVID-19. Review articles are excluded from this waiver policy. Sign up here as a reviewer to help fast-track new submissions.