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

Description

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

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

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:

Technical Notes

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).

References

Last update: 18 May 2016