Tsai 2010, TRIM24, estrogen receptor and H3K4me2 in estrogen-treated and -untreated MCF7 cells

ChIP-seq against ER, TRIM24 and H3K4me2 in estrogen treated and untreated MCF7 cells. Includes total genomic DNA sample as control.

• Raw data was downloaded from GEO series: GSE24166
• Input file format: SRA

From H. sapiens (March 2006 NCBI36/hg18).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM594602.sga	MCF7 ER treated	ER	GSM594602
2	GSM594603.sga	MCF7 ER untreated	ER	GSM594603
3	GSM594604.sga	MCF7 T24 treated	T24	GSM594604
4	GSM594605.sga	MCF7 T24 untreated	T24	GSM594605
5	GSM594606.sga	MCF7 H3K4me2 treated	H3K4me2	GSM594606
6	GSM594607.sga	MCF7 H3K4me2 untreated	H3K4me2	GSM594607
7	GSM594608.sga	total-DNA	total-DNA	GSM594608

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

• Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W, Aronow B, Gozani O, Fischle W, Hung MC, Patel DJ, Barton MC. TRIM24 links a non-canonical histone signature to breast cancer. Nature. 2010 Dec 16;468(7326):927-32. doi: 10.1038/nature09542. 21164480
• GEO series GSE24166: Chromatin enrichment of TRIM24, estrogen receptor and H3K4me2 in estrogen-treated and -untreated MCF7 cells