Zwart 2013, ERalpha ChIP-seq from breast cancer core needle biopsies

Description

ChIP-seq against Estrogen Receptor alpha (ERalpha) in breast cancer biopsies and MCF7 cell line.
Tow carriers (glycogen and human mRNA in combination with recombinant Histone 2B) were incorporated to extract chromatin from a limited amount of starting material.
MCF7 data were produced using 10'000 cells, except those labeled 'saturated' for which 20 millions cells were used.

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 ERR235707.sga breast_cancer|BIOPSY234|ERalpha|Glycogen ERalpha -
2 ERR235702.sga breast_cancer|BIOPSY234|ERalpha|None ERalpha -
3 ERR235709.sga breast_cancer|BIOPSY235|ERalpha|Glycogen ERalpha -
4 ERR235710.sga breast_cancer|BIOPSY235|ERalpha|None ERalpha -
5 ERR235701.sga breast_cancer|BIOPSY3691|ERalpha|mRNA+histone ERalpha -
6 ERR235699.sga breast_cancer|BIOPSY3691|ERalpha|None ERalpha -
7 ERR235705.sga breast_cancer|BIOPSY7367|ERalpha|mRNA+histone ERalpha -
8 ERR235703.sga breast_cancer|BIOPSY7367|ERalpha|None ERalpha -
9 ERR235700.sga MCF7|ERalpha|mRNA+histone ERalpha -
10 ERR235704.sga MCF7|ERalpha|None_1 ERalpha -
11 ERR235706.sga MCF7|ERalpha|None_2 ERalpha -
12 ERR235698.sga MCF7|ERalpha|Saturated_1 ERalpha -
13 ERR235708.sga MCF7|ERalpha|Saturated_2 ERalpha -

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 bed2sga.pl (ChIP-Seq v. 1.5.2).
The peak files are those deposited by the authors. The peak coordinates were lift over to hg19 genome assembly using UCSC liftOver tool.

References

Last update: 4 May 2016