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).



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

Technical Notes

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 (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018