Starick 2015, Glucocorticoid receptor ChIP-exo and ChIP-seq in 3 cell lines.

Glucocorticoid receptor (GR) DNA-binding sites identified using ChIP-seq and ChIP-exo performed in three cell lines: IMR90, U2OS osteosarcoma cell line and K562, upon glucocorticoid treatment. Include untreated cell as control. (Input)

• Raw data was downloaded from: ArrayExpress E-MTAB-2955 E-MTAB-2956 series
• Input file format: BAM
• Download date: 15-3-2017

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	IMR90_GR_ChIP-exo.sga	IMR90|GR|ChIP-exo	GR	-
2	IMR90_GR_ChIP-seq_rep1.sga	IMR90|GR|ChIP-seq	GR	-
3	IMR90_Input_ChIP-seq_rep1.sga	IMR90|Input|ChIP-seq	Input	-
4	K562_GR_ChIP-exo.sga	K562|GR|ChIP-exo	GR	-
5	K562_GR_ChIP-seq_rep1.sga	K562|GR|ChIP-seq	GR	-
6	K562_Input_ChIP-seq_rep1.sga	K562|Input|ChIP-seq	Input	-
7	U2OS_GR_ChIP-exo.sga	U2OS|GR|ChIP-exo	GR	-
8	U2OS_GR_ChIP-seq.sga	U2OS|GR|ChIP-seq	GR	-
9	U2OS_Input_ChIP-seq.sga	U2OS|Input|ChIP-seq	Input	-

BAM files were converted to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

• Starick SR, Ibn-Salem J, Jurk M, Hernandez C, Love MI, Chung HR, Vingron M, Thomas-Chollier M, Meijsing SH
  ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Res. 2015 Jun;25(6):825-35. doi: 10.1101/gr.185157.114. Epub 2015 Feb 26. 25720775