Sikora 2014, ChIP-seq of ER in Invasive Lobular Carcinoma.

Breast cancer cell line MDA-MB-134 was subject to ChIP-seq for the Estrogen Receptor protein (ER). Four samples were used: Estrogen-treated (in the form of 17β-Estradiol) cells followed by ER (ER-α) IP, estrogen treated cells followed by IgG (rabbit origin) IP, EtOH treated cells followed by ER IP and Input (MCF7 genomic DNA).

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 29-6-2017

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1235008.sga	MDA-MB-134|ER|Estrogen|	E-ER	GSM1235008
2	GSM1235010.sga	MDA-MB-134|ER|EtOH|	V-ER	GSM1235010
3	GSM1235009.sga	MDA-MB-134|IgG|Estrogen|	E-IgG	GSM1235009
4	GSM1235011.sga	MDA-MB-134|Input|None|	Input	GSM1235011

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. 1.5.3).

• Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR, Davidson NE, Dabbs DJ, Welm AL, Oesterreich S
  Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Res. 2014 Mar 1;74(5):1463-74. doi: 10.1158/0008-5472.CAN-13-2779. Epub 2014 Jan 14. 24425047
• GEO series GSE51022: ChIP-seq of MDA-MB-134 cell line