Chi 2019, ChIP-seq against ESR1, GRHL2 and H3K27ac in normal breast cells, tumors and MCF7.

Description

This series contains data from ChIP-seq assays applied to normal ER+ mature luminal mammary epithelial cells, ER+ breast tumors, breast cancer cell lines (T47D AND MCF7) and a CRISPR-mediated GRHL2 knockout of MCF7 cells.

ESR1 binding was analyzed in all samples, H3K27ac in tumors only, and GRHL2 in T47D and unmodified MCF7 cells only. For some samples peak lists generated by the authors are also included in this series.

Clinical information on normal breast tissue and breast tumor donors can be be found at PNAS online at:

see Table S1.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 ChIPseq_GRHL2_T47D_WT_Veh_45mins_rep2.sga T47D|GRHL2|Veh_45min|rep2 GRHL2 GSM3595422
2 ChIPseq_GRHL2_T47D_WT_Veh_45mins_rep1.sga T47D|GRHL2|Veh_45min|rep1 GRHL2 GSM3595421
3 ChIPseq_INPUT_MCF7.sga MCF7|Input Input GSM3595420
4 ChIPseq_GRHL2_MCF7_WT_Veh_45mins_rep2.sga MCF7|GRHL2|Veh_45min|rep2 GRHL2 GSM3595419
5 ChIPseq_GRHL2_MCF7_WT_Veh_45mins_rep1.sga MCF7|GRHL2|Veh_45min|rep1 GRHL2 GSM3595418
6 ChIPseq_ER_MCF7_CRISPR_GRHL2_Veh_45min_rep2.sga MCF7_CRISPR_GRHL2|ESR1|Veh_45min|rep2 ESR1 GSM3595417
7 ChIPseq_ER_MCF7_CRISPR_GRHL2_E2_45min_rep2.sga MCF7_CRISPR_GRHL2|ESR1|E2_45min|rep2 ESR1 GSM3595416
8 ChIPseq_ER_MCF7_CRISPR_GRHL2_Veh_45min_rep1.sga MCF7_CRISPR_GRHL2|ESR1|Veh_45min|rep1 ESR1 GSM3595415
9 ChIPseq_ER_MCF7_CRISPR_GRHL2_E2_45min_rep1.sga MCF7_CRISPR_GRHL2|ESR1|E2_45min|rep1 ESR1 GSM3595414
10 ChIPseq_ER_MCF7_WT_Veh_45min_rep2.sga MCF7|ESR1|Veh_45min|rep2 ESR1 GSM3595413
11 ChIPseq_ER_MCF7_WT_E2_45min_rep2.sga MCF7|ESR1|E2_45min|rep2 ESR1 GSM3595412
12 ChIPseq_ER_MCF7_WT_Veh_45min_rep1.sga MCF7|ESR1|Veh_45min|rep1 ESR1 GSM3595411
13 ChIPseq_ER_MCF7_WT_E2_45min_rep1.sga MCF7|ESR1|E2_45min|rep1 ESR1 GSM3595410
14 N1_13-12ML_ER16_S6_ChIP-seq.sga Breast normal N1|ESR1|E2_45min ESR1 GSM2654083
15 N7_20140909-13-89ML-E2_INPUT_DC1247_S2_R1_Control_INPUT.sga Breast normal N7|Input|E2_45min Input GSM2654082
16 N7_20140909-13-89ML-E2-ER-DC1247_S1_R1_ChIP-seq.sga Breast normal N7|ESR1|E2_45min ESR1 GSM2654081
17 N12_12-37ML_INPUT_16_S3_Control_INPUT.sga Breast normal N12|Input|E2_45min Input GSM2654080
18 N12_12-37ML_ER15_S1_ChIP-seq.sga Breast normal N12|ESR1|E2_45min ESR1 GSM2654079
19 N3_12-36ML_INPUT_S1_Control_INPUT.sga Breast normal N3|Input|E2_45min Input GSM2654078
20 N3_12-36ML_ER_S2_ChIP-seq.sga Breast normal N3|ESR1|E2_45min ESR1 GSM2654077
21 N11_12-31ML_INPUT_S9_Control_INPUT.sga Breast normal N11|Input|E2_45min Input GSM2654076
22 N11_12-31ML_ER_S7_ChIP-seq.sga Breast normal N11|ESR1|E2_45min ESR1 GSM2654075
23 T15_JG14B_11.4.15-Control-INPUT.sga Breast tumor T15|Input Input GSM2654074
24 T13_JG13B-Control-INPUT.sga Breast tumor T13|Input Input GSM2654073
25 T8_JG8B-Control-INPUT.sga Breast tumor T8|Input Input GSM2654072
26 T6_JG6B-1-Control-INPUT.sga Breast tumor T6|Input Input GSM2654071
27 T3-rep2-Control-INPUT.sga Breast tumor T3|Input|rep2 Input GSM2654070
28 T3-rep1_11.4.15-Control-INPUT.sga Breast tumor T3|Input|rep1 Input GSM2654069
29 T14_JG7B-Control-INPUT.sga Breast tumor T14|Input Input GSM2654068
30 T12_JG15B-Control-INPUT.sga Breast tumor T12|Input Input GSM2654067
31 T11_JG11B-Control-INPUT.sga Breast tumor T11|Input Input GSM2654066
32 T10_JG10B-Control-INPUT.sga Breast tumor T10|Input Input GSM2654065
33 T9_JG9B-Control-INPUT.sga Breast tumor T9|Input Input GSM2654064
34 T7_JG10A-Control-INPUT.sga Breast tumor T7|Input Input GSM2654063
35 T5_JG5B-1-Control-INPUT.sga Breast tumor T5|Input Input GSM2654062
36 T4_JG4B-2-Control-INPUT.sga Breast tumor T4|Input Input GSM2654061
37 T3_JG3B-2-Control-INPUT.sga Breast tumor T3|Input Input GSM2654060
38 T2_JG2B-Control-INPUT.sga Breast tumor T2|Input Input GSM2654059
39 T15_IdxD1_JG14B_H3K27acChIP_11.4.15-ChIP-seq.sga Breast tumor T15|H3K27ac H3K27ac GSM2654058
40 T14_JG7B_H3K27acChIP_IDX22-ChIP-seq.sga Breast tumor T14|H3K27ac H3K27ac GSM2654057
41 T13_JG13B_H3K27acChIP_IDX8-ChIP-seq.sga Breast tumor T13|H3K27ac H3K27ac GSM2654056
42 T12_JG15B_H3K27acChIP_IDX12-ChIP-seq.sga Breast tumor T12|H3K27ac H3K27ac GSM2654055
43 T11_JG11B_H3K27acChIP_IDX5-ChIP-seq.sga Breast tumor T11|H3K27ac H3K27ac GSM2654054
44 T10_JG10B_H3K27acChIP_IDX4-ChIP-seq.sga Breast tumor T10|H3K27ac H3K27ac GSM2654053
45 T9_JG9B_H3K27acChIP_IDX2-ChIP-seq.sga Breast tumor T9|H3K27ac H3K27ac GSM2654052
46 T8_JG8B_H3K27acChIP_IDX24-ChIP-seq.sga Breast tumor T8|H3K27ac H3K27ac GSM2654051
47 T6_JG6B-1_H3K27acChIP_IDX20-ChIP-seq.sga Breast tumor T6|H3K27ac H3K27ac GSM2654050
48 T5_JG5B-1_H3K27acChIP_IDX18-ChIP-seq.sga Breast tumor T5|H3K27ac H3K27ac GSM2654049
49 T4_JG4B-2_H3K27acChIP_IDX16-ChIP-seq.sga Breast tumor T4|H3K27ac H3K27ac GSM2654048
50 T3-rep3_JG3B-2_H3K27acChIP_IDX14-ChIP-seq.sga Breast tumor T3|H3K27ac|rep3 H3K27ac GSM2654047
51 T3-rep2_IdxA2_JG3B_Breast_H3K27ac_11.24.15-ChIP-seq.sga Breast tumor T3|H3K27ac|rep2 H3K27ac GSM2654046
52 T3-rep1_IdxC1_JG3B_H3K27acChIP_11.4.15-ChIP-seq.sga Breast tumor T3|H3K27ac|rep1 H3K27ac GSM2654045
53 T14_JG7B_ERChIP_IDX14-ChIP-seq.sga Breast tumor T14|ESR1 ESR1 GSM2654044
54 T12_JG15B_ERChIP_IDX6-ChIP-seq.sga Breast tumor T12|ESR1 ESR1 GSM2654043
55 T11_JG11B_ERChIP_IDX22-ChIP-seq.sga Breast tumor T11|ESR1 ESR1 GSM2654042
56 T10_JG10B_ERChIP_IDX20-ChIP-seq.sga Breast tumor T10|ESR1 ESR1 GSM2654041
57 T9_JG9B_ERChIP_IDX18-ChIP-seq.sga Breast tumor T9|ESR1 ESR1 GSM2654040
58 T7_JG10A_ERChIP_IDX19-ChIP-seq.sga Breast tumor T7|ESR1 ESR1 GSM2654039
59 T5_JG5B-1_ERChIP_IDX10-ChIP-seq.sga Breast tumor T5|ESR1 ESR1 GSM2654038
60 T4_JG4B-2_ERChIP_IDX8-ChIP-seq.sga Breast tumor T4|ESR1 ESR1 GSM2654037
61 T3_JG3B-2_ERChIP_IDX6-ChIP-seq.sga Breast tumor T3|ESR1 ESR1 GSM2654036
62 T2_JG2B_ERChIP_IDX4-ChIP-seq.sga Breast tumor T2|ESR1 ESR1 GSM2654035

ChIP-seq peaks files:

Filename Description Feature GEO-ID
1 GSM2654035_JG2B_ERChIP_sort_peaks.narrowPeak.sga Breast tumor T2|ESR1 ESR1_P GSM2654035
2 GSM2654036_JG3B-2-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T3|ESR1 ESR1_P GSM2654036
3 GSM2654037_JG4B-2-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T4|ESR1 ESR1_P GSM2654037
4 GSM2654038_JG5B-1-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T5|ESR1 ESR1_P GSM2654038
5 GSM2654039_JG10A-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T7|ESR1 ESR1_P GSM2654039
6 GSM2654040_JG9B-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T9|ESR1 ESR1_P GSM2654040
7 GSM2654041_JG10B-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T10|ESR1 ESR1_P GSM2654041
8 GSM2654042_JG11B-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T11|ESR1 ESR1_P GSM2654042
9 GSM2654043_JG15B-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T12|ESR1 ESR1_P GSM2654043
10 GSM2654044_JG7B-ERChIP_sort_peaks.narrowPeak.sga Breast tumor T14|ESR1 ESR1_P GSM2654044
11 GSM3595410_ER_MCF7_control_1_E2_45_min_sort_peaks.narrowPeak.sga MCF7|ESR1|E2_45min|rep1 ESR1_P GSM3595410
12 GSM3595411_ER_MCF7_control_1_veh_45_min_sort_peaks.narrowPeak.sga MCF7|ESR1|Veh_45min|rep1 ESR1_P GSM3595411
13 GSM3595412_ER_MCF7_control_2_E2_45_min_sort_peaks.narrowPeak.sga MCF7|ESR1|E2_45min|rep2 ESR1_P GSM3595412
14 GSM3595413_ER_MCF7_control_2_veh_45_min_sort_peaks.narrowPeak.sga MCF7|ESR1|Veh_45min|rep2 ESR1_P GSM3595413
15 GSM3595414_ER_MCF7_GRHL2_1_E2_45_min_sort_peaks.narrowPeak.sga MCF7_CRISPR_GRHL2|ESR1|E2_45min|rep1 GRHL2_P GSM3595414
16 GSM3595415_ER_MCF7_GRHL2_1_veh_45_min_sort_peaks.narrowPeak.sga MCF7_CRISPR_GRHL2|ESR1|Veh_45min|rep1 GRHL2_P GSM3595415
17 GSM3595416_ER_MCF7_GRHL2_2_E2_45_min_sort_peaks.narrowPeak.sga MCF7_CRISPR_GRHL2|ESR1|E2_45min|rep2 GRHL2_P GSM3595416
18 GSM3595417_ER_MCF7_GRHL2_2_veh_45_min_sort_peaks.narrowPeak.sga MCF7_CRISPR_GRHL2|ESR1|Veh_45min|rep2 GRHL2_P GSM3595417
19 GSM3595418_HARI_GRHL2_V_6_15_MCF7_-3_sort_peaks.narrowPeak.sga MCF7|GRHL2|Veh_45min|rep1 GRHL2_P GSM3595418
20 GSM3595419_HARI_GRHL2_V_6_15_MCF7_-4_sort_peaks.narrowPeak.sga MCF7|GRHL2|Veh_45min|rep2 GRHL2_P GSM3595419
21 GSM3595421_HARI_GRHL2_E2_6_16_T47D_-2_sort_peaks.narrowPeak.sga T47D|GRHL2|Veh_45min|rep1 GRHL2_P GSM3595421
22 GSM3595422_HARI_GRHL2_V_6_16_T47D_-1_sort_peaks.narrowPeak.sga T47D|GRHL2|Veh_45min|rep2 GRHL2_P GSM3595422

Quality Control and Ananylsis

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).

Note that some raw data (SRA) files from this series contain single-end sequences while others contain paired-end sequences. However, since some paired-samples yielded low alignment efficiency, all samples were mapped in single-end mode to the genome.

Peak lists: Only peak lists provided in narrowPeak format were imported. narrowPeak to SGA conversion was carried out using bed2sga. Field 7 (singalValue) from the input files was transferred to optional filed 6 of the output files.

References

Last update: 16 Nov 2020