Jozwik 2016, FOXA1 and MLL3 maps in breast cancer cells.


ChIPseq of MLL3, FOXA1, GRHL2, H3K4me3, H3K4me1 in asynchronous MCF7 cells.



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

ChIP-seq data:

Filename Description Feature GEO-ID
1 MLL3_No_treatment.sga MCF7|MLL3|No treatment|All Rep MLL3 -
2 GSM2171859.sga MCF7|MLL3|No treatment|rep0 MLL3 GSM2171859
3 GSM2171860.sga MCF7|MLL3|No treatment|rep1 MLL3 GSM2171860
4 GSM2171861.sga MCF7|MLL3|No treatment|rep2 MLL3 GSM2171861
5 GSM2171862.sga MCF7|MLL3|No treatment|rep3 MLL3 GSM2171862
6 MLL3_FOXA1_siRNA.sga MCF7|MLL3|FOXA1 siRNA|All Rep MLL3 -
7 GSM2171856.sga MCF7|MLL3|FOXA1 siRNA|Rep1 MLL3 GSM2171856
8 GSM2171857.sga MCF7|MLL3|FOXA1 siRNA|Rep2 MLL3 GSM2171857
9 GSM2171858.sga MCF7|MLL3|FOXA1 siRNA|Rep3 MLL3 GSM2171858
10 MLL3_Nonspecific_siRNA.sga MCF7|MLL3|Nonspecific siRNA|All Rep MLL3 -
11 GSM2171853.sga MCF7|MLL3|Nonspecific siRNA|Rep1 MLL3 GSM2171853
12 GSM2171854.sga MCF7|MLL3|Nonspecific siRNA|Rep2 MLL3 GSM2171854
13 GSM2171855.sga MCF7|MLL3|Nonspecific siRNA|Rep3 MLL3 GSM2171855
14 GSM2171833.sga MCF7|FOXA1|No treatment FOXA1 GSM2171833
15 FOXA1_Nonspecific_siRNA.sga MCF7|FOXA1|Nonspecific siRNA|All rep FOXA1 -
16 GSM2171829.sga MCF7|FOXA1|Nonspecific siRNA|Rep0 FOXA1 GSM2171829
17 GSM2171830.sga MCF7|FOXA1|Nonspecific siRNA|Rep1 FOXA1 GSM2171830
18 GSM2171831.sga MCF7|FOXA1|Nonspecific siRNA|Rep2 FOXA1 GSM2171831
19 GSM2171832.sga MCF7|FOXA1|Nonspecific siRNA|Rep3 FOXA1 GSM2171832
20 GRHL2_No_treatment.sga MCF7|GRHL2|No treatment|All rep GRHL2 -
21 GSM2171834.sga MCF7|GRHL2|No treatment|Rep2 GRHL2 GSM2171834
22 GSM2171835.sga MCF7|GRHL2|No treatment|Rep3 GRHL2 GSM2171835
23 GSM2171836.sga MCF7|GRHL2|No treatment|Rep1 GRHL2 GSM2171836
24 H3K4me1_MLL3_siRNA.sga MCF7|H3K4me1|MLL3 siRNA|All rep H3K4me1 -
25 GSM2171841.sga MCF7|H3K4me1|MLL3 siRNA|Rep0 H3K4me1 GSM2171841
26 GSM2171842.sga MCF7|H3K4me1|MLL3 siRNA|rep1 H3K4me1 GSM2171842
27 GSM2171843.sga MCF7|H3K4me1|MLL3 siRNA|Rep2 H3K4me1 GSM2171843
28 GSM2171844.sga MCF7|H3K4me1|MLL3 siRNA|Rep3 H3K4me1 GSM2171844
29 H3K4me1_Nonspecific_siRNA.sga MCF7|H3K4me1|Nonspecific siRNA|All rep H3K4me1 -
30 GSM2171837.sga MCF7|H3K4me1|Nonspecific siRNA|Rep0 H3K4me1 GSM2171837
31 GSM2171838.sga MCF7|H3K4me1|Nonspecific siRNA|Rep1 H3K4me1 GSM2171838
32 GSM2171839.sga MCF7|H3K4me1|Nonspecific siRNA|Rep2 H3K4me1 GSM2171839
33 GSM2171840.sga MCF7|H3K4me1|Nonspecific siRNA|Rep3 H3K4me1 GSM2171840
34 H3K4me3_MLL3_siRNA.sga MCF7|H3K4me3|MLL3 siRNA|All rep H3K4me3 -
35 GSM2171849.sga MCF7|H3K4me3|MLL3 siRNA|rep1 H3K4me3 GSM2171849
36 GSM2171850.sga MCF7|H3K4me3|MLL3 siRNA|rep2 H3K4me3 GSM2171850
37 GSM2171851.sga MCF7|H3K4me3|MLL3 siRNA|rep3 H3K4me3 GSM2171851
38 GSM2171852.sga MCF7|H3K4me3|MLL3 siRNA|rep4 H3K4me3 GSM2171852
39 H3K4me3_Nonspecific_siRNA.sga MCF7|H3K4me3|Nonspecific siRNA|All rep H3K4me3 -
40 GSM2171845.sga MCF7|H3K4me3|Nonspecific siRNA|rep1 H3K4me3 GSM2171845
41 GSM2171846.sga MCF7|H3K4me3|Nonspecific siRNA|rep2 H3K4me3 GSM2171846
42 GSM2171847.sga MCF7|H3K4me3|Nonspecific siRNA|rep3 H3K4me3 GSM2171847
43 GSM2171848.sga MCF7|H3K4me3|Nonspecific siRNA|rep4 H3K4me3 GSM2171848
44 GSM2171865.sga MCF7|input|No treatment input GSM2171865
45 GSM2171863.sga MCF7|input|Nonspecific siRNA|rep2 input GSM2171863
46 GSM2171864.sga MCF7|input|Nonspecific siRNA|rep3 input GSM2171864

ChIP-seq peaks files:

Filename Description Feature GEO-ID
1 GSE81714_foxa1_sict-sict_input_peaks.narrowPeak.sga MCF7|FOXA1|Nonspecific siRNA|Peaks FOXA1 -
2 GSE81714_foxa1_untreated-mcf7_input_peaks.narrowPeak.sga MCF7|FOXA1|No treatment|Peaks FOXA1 -
3 GSE81714_grhl2_untreated-mcf7_input_peaks.narrowPeak.sga MCF7|GRHL2|No treatment|Peaks GRHL2 -
4 GSE81714_h3k4me1_sict-sict_input_peaks.broadPeak.sga MCF7|H3K4ME1|Nonspecific siRNA|Peaks H3K4ME1 -
5 GSE81714_h3k4me1_simll3-sict_input_peaks.broadPeak.sga MCF7|H3K4ME1|MLL3 siRNA|Peaks H3K4ME1 -
6 GSE81714_h3k4me3_sict-sict_input_peaks.broadPeak.sga MCF7|H3K4ME3|Nonspecific siRNA|Peaks H3K4ME3 -
7 GSE81714_h3k4me3_simll3-sict_input_peaks.broadPeak.sga MCF7|H3K4ME3|MLL3 siRNA|Peaks H3K4ME3 -
8 GSE81714_mll3_sict-sict_input_peaks.narrowPeak.sga MCF7|MLL3|Nonspecific siRNA|Peaks MLL3 -
9 GSE81714_mll3_sifoxa1-sict_input_peaks.narrowPeak.sga MCF7|MLL3|FOXA1 siRNA|Peaks MLL3 -
10 GSE81714_mll3_untreated-sict_input_peaks.narrowPeak.sga MCF7|MLL3|No treatment|Peaks MLL3 -

Merged samples:

Replicas of the same biological samples were merged ('All rep' samples)

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018