Su 2015, H3K27me3 and H3K27Ac in somatic breast cancer cell hybrids.

ChIP-seq against H3K27me3 and H3K27ac in various breast cancer cell lines. See "Notes on samples nomenclature" below.

• Raw data was downloaded from SRA via GEO SubSeries GSE38788, GSE38789 and GSE69112 . These SubSeries are part of SuperSeries: GSE38548
• Input file format: SRA

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	SRR513994.sga	MDA231|H3K27me3|ABS	H3K27me3	GSM949581
2	SRR514021.sga	MCF7|H3K27me3|IGA	H3K27me3	GSM949575
3	SRR514022.sga	T47D|H3K27me3|IGA	H3K27me3	GSM949576
4	SRR514023.sga	MDA231+MCF7|hybdrid|H3K27me3|IGA	H3K27me3	GSM949577
5	SRR514024.sga	SUM159PT+MCF7 hybrid|H3K27me3|IGA	H3K27me3	GSM949578
6	SRR514025.sga	SUM159PT+T47D hybrid|H3K27me3|IGA	H3K27me3	GSM949579
7	SRR514026.sga	SUM159PT|H3K27me3|run1|IGA	H3K27me3	GSM949580
8	SRR514027.sga	SUM159PT|H3K27me3|run2|IGA	H3K27me3	GSM949580
9	SRR1958719.sga	ZR75|H3K27me3|ABS	H3K27me3	GSM1654342
10	SRR1958720.sga	SUM159+ZR75 hybrid|H3K27me3|ABS	H3K27me3	GSM1654343
11	SRR1958721.sga	CAL51|H3K27me3|ABS	H3K27me3	GSM1654344
12	SRR1958722.sga	CAL51+MCF7 hybrid|H3K27me3|ABS	H3K27me3	GSM1654345
13	SRR1958723.sga	21NT|H3K27me3|ABS	H3K27me3	GSM1654346
14	SRR1958724.sga	SUM159+21NT hybrid|H3K27me3|ABS	H3K27me3	GSM1654347
15	SRR1958725.sga	MDA453|H3K27me3|ABS	H3K27me3	GSM1654348
16	SRR1958726.sga	SUM159+MDA453 hybrid|H3K27me3|ABS	H3K27me3	GSM1654349
17	SRR2035161.sga	CAL51 hybrid|H3K27Ac|INS	H3K27Ac	GSM1693015
18	SRR2035162.sga	CAL51+MCF7 hybrid|H3K27Ac|INS	H3K27Ac	GSM1693016
19	SRR2035163.sga	MCF7|H3K27Ac|INS	H3K27Ac	GSM1693017
20	SRR2035164.sga	MDA231|H3K27Ac|INS	H3K27Ac	GSM1693018
21	SRR2035165.sga	MDA231+MCF7 hybrid|H3K27Ac|INS	H3K27Ac	GSM1693019
22	SRR2035166.sga	SUM159+BT474 hybrid|H3K27Ac|INS	H3K27Ac	GSM1693020
23	SRR2035167.sga	SUM159|H3K27Ac|INS	H3K27Ac	GSM1693021
24	SRR2035168.sga	SUM159+MCF7 hybrid|H3K27Ac|INS	H3K27Ac	GSM1693022
25	SRR2035169.sga	SUM159+T47D hybrid|H3K27Ac|INS	H3K27Ac	GSM1693023
26	SRR2035170.sga	SUM159+ZR75 hybrid|H3K27Ac|INS	H3K27Ac	GSM1693024
27	SRR2035171.sga	T47D|H3K27Ac|INS	H3K27Ac	GSM1693025
28	SRR2035172.sga	ZR75|singe|H3K27Ac|INS	H3K27Ac	GSM1693026
29	SRR2035173.sga	CAL51|Input|INS	Input	GSM1693027
30	SRR2035174.sga	CAL51+MCF7 hybrid|Input|INS	Input	GSM1693028
31	SRR2035175.sga	MCF7|Inpu|INSt	Input	GSM1693029
32	SRR2035176.sga	MDA231|Input|INS	Input	GSM1693030
33	SRR2035177.sga	MDA231+MCF7 hybrid|Input|INS	Input	GSM1693031
34	SRR2035178.sga	SUM159+BT474 hybrid|Input|INS	Input	GSM1693032
35	SRR2035179.sga	SUM159+MCF7 hybrid|Input|INS	Input	GSM1693033
36	SRR2035180.sga	SUM159+T47D hybrid|Input|INS	Input	GSM1693034
37	SRR2035181.sga	SUM159+ZR75 hybrid|Input|INS	Input	GSM1693035
38	SRR2035182.sga	T47D|Input|INS	Input	GSM1693036
39	SRR2035183.sga	ZR75|singe|Input|INS	Input	GSM1693037

Notes on samples nomenclature:

• The cell line of origin can be retrieved from the description field, e.g. 'SUM159+ZR75|hybrid|H3K27me3' means that this sample comes from a fusion between SUM159 and ZR75 cells.
• The 'hybrid' label asserts that this sample comes from a fusion event, otherwise, the label is 'single'.
• Each sample has been single-end sequenced using a different plateform. The three different plateforms used are : Illumina Genome Analyzer (labelled 'IGA'), AB SOLiD 4 System (labelled 'ABS') and Illumina NextSeq500 (labelled 'INS'). This information is also present in the description field.

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg19 genome using Bowtie 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. 1.5.2).

• Su Y, Subedee A, Bloushtain-Qimron N, Savova V, Krzystanek M, Li L, Marusyk A, Tabassum DP, Zak A, Flacker MJ, Li M, Lin JJ, Sukumar S, Suzuki H, Long H, Szallasi Z, Gimelbrant A, Maruyama R, Polyak K
  Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer. Cell Rep. 2015 Jun 16;11(10):1549-63. doi: 10.1016/j.celrep.2015.05.011. Epub 2015 Jun 4. 26051943