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).
FASTQ files were extracted from SRA files using fastq-dump
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
Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR,
Davidson NE, Dabbs DJ, Welm AL, Oesterreich S
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
ChIP-seq of MDA-MB-134 cell line