Ghahhari 2022, ChIP-seq against ESR1 in ZEB1 expressing MCF-V cells.


ChIP-seq of estrogen receptor α in wild type MCF7-V breast carcinoma cell line and in MCF7-V cells transduced with a doxycyline-inducible construct to express ZEB1. ChIP-seq assays in doxycyline treated were performed after E2 or FI treatment or no treatment as control. FI is a cocktail composed of forskolin (to stimulate adenylate cyclase) and 3-isobutyl-1-methylxanthine (to block phosphodiesterase).



From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM5268458_ESR1_Ctl_rep1.sga MCF7-V:trans-ZEB1|ESR1|+DOX/Ctl|rep1 ESR1 GSM5268458
2 GSM5268459_ESR1_Ctl_rep2.sga MCF7-V:trans-ZEB1|ESR1|+DOX/Ctl|rep2 ESR1 GSM5268459
3 GSM5268460_ESR1_Ctl_rep3.sga MCF7-V:trans-ZEB1|ESR1|+DOX/Ctl|rep3 ESR1 GSM5268460
4 GSM5268461_ESR1_Ctl_rep4.sga MCF7-V:trans-ZEB1|ESR1|+DOX/Ctl|rep4 ESR1 GSM5268461
5 GSM5268462_ESR1_E2_rep1.sga MCF7-V:trans-ZEB1|ESR1|+DOX/E2|rep1 ESR1 GSM5268462
6 GSM5268463_ESR1_E2_rep2.sga MCF7-V:trans-ZEB1|ESR1|+DOX/E2|rep2 ESR1 GSM5268463
7 GSM5268464_ESR1_E2_rep3.sga MCF7-V:trans-ZEB1|ESR1|+DOX/E2|rep3 ESR1 GSM5268464
8 GSM5268465_ESR1_E2_rep4.sga MCF7-V:trans-ZEB1|ESR1|+DOX/E2|rep4 ESR1 GSM5268465
9 GSM5268466_ESR1_FI_rep1.sga MCF7-V:trans-ZEB1|ESR1|+DOX/FI|rep1 ESR1 GSM5268466
10 GSM5268467_ESR1_FI_rep2.sga MCF7-V:trans-ZEB1|ESR1|+DOX/FI|rep2 ESR1 GSM5268467
11 GSM5268468_ESR1_FI_rep3.sga MCF7-V:trans-ZEB1|ESR1|+DOX/FI|rep3 ESR1 GSM5268468
12 GSM5268469_ESR1_FI_rep4.sga MCF7-V:trans-ZEB1|ESR1|+DOX/FI|rep4 ESR1 GSM5268469
13 GSM5268458_ESR1_Ctl_merged.sga MCF7-V:trans-ZEB1|ESR1|+DOX/Ctl|all ESR1 GSE173479
14 GSM5268462_ESR1_E2_merged.sga MCF7-V:trans-ZEB1|ESR1|+DOX/E2|all ESR1 GSE173479
15 GSM5268466_ESR1_FI_merged.sga MCF7-V:trans-ZEB1|ESR1|+DOX/FI|all ESR1 GSE173479

Notes on samples nomenclature:
Merged samples:

Replicates of the same experiments were merged. Merged SGA files are provided in addition to the individual replicate files.

Quality Control and Analysis

The scripts for generating the QC and analysis plots can be found here: ghahhari22_analysis.tar.gz

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.2.2. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.5).

For reproducibility purposes, the scripts used for generating the SGA files are posted here: ghahhari22_scripts.tar.gz


Last update: 21 Oct 2022
Page made by: Philipp Bucher