GSE31363, Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago.

ChIP-seq data against Epotope-tagged transcription factors expressed as GFP-fusion proteins in K562 cells. The data were produced by the University of Chicago as part of the ENCODE project.

The source data were downloaded from ENCODE at UCSC

• Raw data was downloaded from: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUchicagoTfbs/
• Input file format: BAM, BED (narrowPeak
• Download date: 17-10-2018

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	EH001207_rep1.sga	K562|FOS-EGFP||UChicago rep1	FOS	GSM777644
2	EH001207_rep2.sga	K562|FOS-EGFP||UChicago rep2	FOS	GSM777644
3	EH001207_rep3.sga	K562|FOS-EGFP||UChicago rep3	FOS	GSM777644
4	EH001208_rep1.sga	K562|GATA2-EGFP||UChicago rep1	GATA2	GSM777641
5	EH001208_rep2.sga	K562|GATA2-EGFP||UChicago rep2	GATA2	GSM777641
6	EH001209_rep1.sga	K562|HDAC8-EGFP||UChicago rep1	HDAC8	GSM777640
7	EH001209_rep2.sga	K562|HDAC8-EGFP||UChicago rep2	HDAC8	GSM777640
8	EH001201_rep1.sga	K562|Input (FOS)|UChicago rep1	Input	GSM777646
9	EH001201_rep2.sga	K562|Input (FOS)|UChicago rep2	Input	GSM777646
10	EH001201_rep3.sga	K562|Input (FOS)|UChicago rep3	Input	GSM777646
11	EH001202_rep1.sga	K562|Input (GATA2)|UChicago rep1	Input	GSM777648
12	EH001202_rep2.sga	K562|Input (GATA2)|UChicago rep2	Input	GSM777648
13	EH001203_rep1.sga	K562|Input (HDAC8)|UChicago rep1	Input	GSM777647
14	EH001203_rep2.sga	K562|Input (HDAC8)|UChicago rep2	Input	GSM777647
15	EH001204_rep1.sga	K562|Input (JUNB)|UChicago rep1	Input	GSM777643
16	EH001204_rep2.sga	K562|Input (JUNB)|UChicago rep2	Input	GSM777643
17	EH001205_rep1.sga	K562|Input (JUND)|UChicago rep1	Input	GSM777642
18	EH001205_rep2.sga	K562|Input (JUND)|UChicago rep2	Input	GSM777642
19	EH001205_rep3.sga	K562|Input (JUND)|UChicago rep3	Input	GSM777642
20	EH001206_rep1.sga	K562|Input (NR4A1)|UChicago rep1	Input	GSM777645
21	EH001206_rep2.sga	K562|Input (NR4A1)|UChicago rep2	Input	GSM777645
22	EH001210_rep1.sga	K562|JUNB-EGFP||UChicago rep1	JUNB	GSM777638
23	EH001210_rep2.sga	K562|JUNB-EGFP||UChicago rep2	JUNB	GSM777638
24	EH001211_rep1.sga	K562|JUND-EGFP||UChicago rep1	JUND	GSM777639
25	EH001211_rep2.sga	K562|JUND-EGFP||UChicago rep2	JUND	GSM777639
26	EH001211_rep3.sga	K562|JUND-EGFP||UChicago rep3	JUND	GSM777639
27	EH001212_rep1.sga	K562|NR4A1-EGFP||UChicago rep1	NR4A1	GSM777637
28	EH001212_rep2.sga	K562|NR4A1-EGFP||UChicago rep2	NR4A1	GSM777637

ChIP-seq peaks files:

	Filename	Description	Feature	GEO-ID
1	EH001207_narrowPeak.sga	K562|FOS-EGFP narrowPeak||UChicago	FOS_P	GSM777644
2	EH001208_narrowPeak.sga	K562|GATA2-EGFP narrowPeak||UChicago	GATA2_P	GSM777641
3	EH001209_narrowPeak.sga	K562|HDAC8-EGFP narrowPeak||UChicago	HDAC8_P	GSM777640
4	EH001210_narrowPeak.sga	K562|JUNB-EGFP narrowPeak||UChicago	JUNB_P	GSM777638
5	EH001211_narrowPeak.sga	K562|JUND-EGFP narrowPeak||UChicago	JUND_P	GSM777639
6	EH001212_narrowPeak.sga	K562|NR4A1-EGFP narrowPeak||UChicago	NR4A1_P	GSM777637

Notes on samples nomenclature:

All sample information was derived from a file named "files.txt" downloaded from the above-indicated URL. This file contains a list of filenames long with annotation (metadata). The sample descriptions provided here include cell type, ChIP-seq target (transcription factor), treatment and replicate. Cell types and treatments were transferred from ENCODE annotation as such. Some of the original ChIP-seq target names were modified in order to conform to the naming conventions of the MGA repository. Epitop-tagged transcription factors are identified by the corresponding HGNC gene symbol followed by the name of the epitope name, e.g. JUND-EGFP.

The sample descriptions provided here were required to be unique across all ENCODE data series of the MGA repository. For this reason, the name of data contributing lab is indicated in the replicate field. Note further that the names of the local data files contain as first part the experiment identifier (dccAccession) extracted from the ENCODE annotation file. This identifier makes it possible to match a data file from this series to the corresponding peak list in hg19/encode/Uniform_TFBS.

More information about cell lines, antibodies, treatments, protocols, etc. can be found at https://genome.ucsc.edu/encode/otherTerms.html.

Optional fields in SGA files:

The peak files contain in the optional sixth field a positive real number reflecting the overall enrichment of the ChIP-seq signal in the peak region.

Files with a non-empty objectStatus in the file list provided by UCSC were not considered. BAM files were converted into BED using bamToBed (bedtools v2.27.0) and subsequently converted into SGA using bed2sga ( ChIP-Seq v. 1.5.3). Peak files in narrowPeak format were converted into SGA using bed2sga with options --narrowPeak -e 7.

• ENCODE Project Consortium
  An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. 22955616
• GEO series GSE31363: Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago

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