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).

• Raw data was downloaded from SRA, bioproject: PRJNA725807
• Input file format: FASTQ
• Download date: 21-10-2022

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:

+DOX: doxocycline treatment to induce ZEB1 expression
Ctl: control (treatment with DMSO)
E2: treatment with 17-beta estradiol (E2)
FI: treatment with Forskolin + 3-isobutyl-1-methylxanthine (IBMX)

Merged samples:

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

• Strand correlation plots: ghahhari22_strand_cor.pdf
• ChIP-seq tag enrichment around bound ESR1 sites. ghahhari22_motif_enr.pdf

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

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

• Mohammadi Ghahhari N, Sznurkowska MK, Hulo N, Bernasconi L, Aceto N, Picard D. Cooperative interaction between ERα and the EMT-inducer ZEB1 reprograms breast cancer cells for bone metastasis. Nat Commun. 2022 Apr 19;13(1):2104. doi: 10.1038/s41467-022-29723-5. PMID: 35440541
• GEO series GSE173479: ChIP-seq of estrogen receptor α in wild type MCF7-V and in MCF7-V breast carcinoma cell line transduced with a doxycyline-inducible construct to express ZEB1.