Singhal 2016, ChIP-seq and reChIP for ESR1 and PGR in hormone treated parental (PR+) and PR- T47D cells.

Description

ChIP-seq against ESR1 and PRG was carried out in ER+PR+ parental T47D cells and PR-deficient T47D cells under different conditions: vehicle, E2 45 min, R5020 45 min and E2R5020 45 min. In addition, ChIP followed by ChIP (reChIP-seq) was carried out in order to map hormone receptor binding sites simultaneously occupied by ESR1 and PRG. Separate input controls are provided for ChIP-seq and reChIP-seq experiments.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 T47D_Vehicle_45_mins_PR_ChIP.sga T47D|PGR|vehicle| PGR GSM2112795
2 T47D_Vehicle_45_mins_ER_ChIP.sga T47D|ESR1|vehicle| ESR1 GSM2112796
3 T47D_E2_45_mins_PR_ChIP.sga T47D|PGR|E2| PGR GSM2112797
4 T47D_E2_45_mins_ER_ChIP.sga T47D|ESR1|E2| ESR1 GSM2112798
5 T47D_R5020_45_mins_PR_ChIP.sga T47D|PGR|R5020| PGR GSM2112799
6 T47D_R5020_45_mins_ER_ChIP.sga T47D|ESR1|R5020| ESR1 GSM2112800
7 T47D_E2R5020_45_mins_PR_ChIP.sga T47D|PGR|E2,R5020| PGR GSM2112801
8 T47D_E2R5020_45_mins_ER_ChIP.sga T47D|ESR1|E2,R5020| ESR1 GSM2112802
9 T47D_Vehicle_45_mins_ERPRComplex_reChIP.sga T47D|ESR1+PGR|vehicle| ESR1_PGR GSM2112803
10 T47D_Vehicle_45_mins_ERIgG_Control_reChIP.sga T47D|ESR1+IgG|vehicle| ESR1_IgG GSM2112804
11 T47D_E2R5020_45_mins_ERPRComplex_reChIP.sga T47D|ESR1+PGR|E2,R5020| ESR1_PGR GSM2112805
12 T47D_E2R5020_45_mins_ERIgG_Control_reChIP.sga T47D|ESR1+IgG|E2,R5020| ESR1_IgG GSM2112806
13 T47D_PR-deficient_Vehicle_45_mins_ER_ChIP.sga T47D PR-|ESR1|vehicle| ESR1 GSM2112807
14 T47D_PR-deficient_E2_45_mins_ER_ChIP.sga T47D PR-|ESR1|E2| ESR1 GSM2112808
15 T47D_PR-deficient_R5020_45_mins_ER_ChIP.sga T47D PR-|ESR1|R5020| ESR1 GSM2112809
16 T47D_PR-deficient_E2R5020_45_mins_ER_ChIP.sga T47D PR-|ESR1|E2,R5020| ESR1 GSM2112810
17 T47D_Vehicle_45_mins_INPUT_ChIP.sga T47D|Input|vehicle| Input GSM2112811
18 T47D_E2_45_mins_INPUT_ChIP.sga T47D|Input|E2| Input GSM2112812
19 T47D_R5020_45_mins_INPUT_ChIP.sga T47D|Input|R5020| Input GSM2112813
20 T47D_E2R5020_45_mins_INPUT_ChIP.sga T47D|Input|E2,R5020| Input GSM2112814
21 T47D_Vehicle_45_mins_INPUT_reChIP.sga T47D|Input|vehicle|reChIP Input GSM2112815
22 T47D_E2R5020_45_mins_INPUT_reChIP.sga T47D|Input|E2,R5020|reChIP Input GSM2112816
23 T47D_PR-deficient_Vehicle_45_mins_INPUT_ChIP.sga T47D PR-|Input|vehicle| Input GSM2112817
24 T47D_PR-deficient_E2_45_mins_INPUT_ChIP.sga T47D PR-|Input|E2| Input GSM2112818
25 T47D_PR-deficient_R5020_45_mins_INPUT_ChIP.sga T47D PR-|Input|R5020| Input GSM2112819
26 T47D_PR-deficient_E2R5020_45_mins_INPUT_ChIP.sga T47D PR-|Input|E2,R5020| Input GSM2112820

Notes on samples nomenclature:

ReChIP-seq samples have target name "ESR1+PRG" in the second field of the target description.

Input controls for reChIP-seq experiments are identified by the tag "reChIP" in the fourth field of the description, which is usually occupied by a replicate identifier. For ChIP-seq samples, this field is left blank.

Quality Control and Analysis

The scripts for generating the QC and analysis plots can be found here: singhal16_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: singhal16_scripts.tar.gz

References

Last update: 18 Feb 2022
Page made by: Philipp Bucher