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.



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:

Quality Control and Analysis

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).


Last update: 21 Dec 2021
Page made by: Philipp Bucher