Nacht 2019, ChIP-seq against PGR, CEBPA, RAD21 and TOP2A in response to progestins and knockdown of CEBPA.

ChIP-seq against PGR, CEBPA, RAD21 and TOP2A in T47D breast cancer cells. Experiments were carried out under different conditions: untreated, progestin (R5020) treated, CEBPA knockdown and control siRNA.

• Raw data was downloaded from SRA: SRP201251, GEO series GSE132649
• Input file format: SRA/FASTQ
• Download date: 16-11-2021

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	T47D_PGR_PR.sga	T47D|PGR|R5020	PGR	GSM3884751
2	T47D_CEBPA_none.sga	T47D|CEBPA|none	CEBPA	GSM3884752
3	T47D_CEBPA_PR.sga	T47D|CEBPA|R5020	CEBPA	GSM3884753
4	T47D_PGR_none.sga	T47D|PGR|none	PGR	GSM3884754
5	T47D_CEBPA_none_siControl.sga	T47D|CEBPA|none,siControl	CEBPA	GSM3884755
6	T47D_CEBPA_none_siCEBPA.sga	T47D|CEBPA|none,siCEBPA	CEBPA	GSM3884756
7	T47D_PGR_none_siControl.sga	T47D|PGR|none,siControl	PGR	GSM3884757
8	T47D_PGR_PR_siControl.sga	T47D|PGR|R5020,siControl	PGR	GSM3884758
9	T47D_PGR_none_siCEBPA.sga	T47D|PGR|none,siCEBPA	PGR	GSM3884759
10	T47D_PGR_PR_siCEBPA.sga	T47D|PGR|R5020,siCEBPA	PGR	GSM3884760
11	T47D_RAD21_none_siControl.sga	T47D|RAD21|none,siControl	RAD21	GSM3884761
12	T47D_RAD21_PR_siControl.sga	T47D|RAD21|R5020,siControl	RAD21	GSM3884762
13	T47D_RAD21_none_siCEBPA.sga	T47D|RAD21|none,siCEBPA	RAD21	GSM3884763
14	T47D_RAD21_PR_siCEBPA.sga	T47D|RAD21|R5020,siCEBPA	RAD21	GSM3884764
15	T47D_TOP2A_none_siControl.sga	T47D|TOP2A|none,siControl	TOP2A	GSM3884765
16	T47D_TOP2A_PR_siControl.sga	T47D|TOP2A|R5020,siControl	TOP2A	GSM3884766
17	T47D_TOP2A_none_siCEBPA.sga	T47D|TOP2A|none,siCEBPA	TOP2A	GSM3884767
18	T47D_TOP2A_PR_siCEBPA.sga	T47D|TOP2A|R5020,siCEBPA	TOP2A	GSM3884768

Notes on samples nomenclature:

R5020: progestin treatment (10 nM R5020) for 6 h

• Strand correlation plots: nacht19_strand_cor.pdf
• ChIP-seq tag enrichment around bound NR3C1 (for PGR), CEBPA or CTCF (for RAD21) motifs, respectively: nacht19_motif_enr.pdf

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).

• Nacht AS, Ferrari R, Zaurin R, Scabia V, Carbonell J, Le Dily F, Quilez J, Leopoldi A, Brisken C, Beato M, Vicent GP.
  CEBPα mediates the growth inhibitory effect of progestins on breast cancer cells. EMBO J. 2019 Sep 16;38(18):e101426. doi: 10.15252/embj.2018101426. Epub 2019 Aug 2. PMID: 31373033
• GEO series GSE132649: C/EBPa mediates the growth inhibitory effect of progestins on breast cancer cells