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

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

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 17-4-2018

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)

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 bed2sga.pl (ChIP-Seq v. 1.5.3).

• Jozwik KM, Chernukhin I, Serandour AA, Nagarajan S, Carroll JS
  FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3. Cell Rep. 2016 Dec 6;17(10):2715-2723. doi: 10.1016/j.celrep.2016.11.028. 27926873
• GEO series GSE81714: FOXA1 directs H3K4 monomethylation at enhancers via recruitment of the methyltransferase MLL3