Locke 2015, Epigenetic remodelling in early breast carcinogenesis

Description

ChIP-seq against histone modifications and DNA-methylation profiles derived with Methylated DNA Binding Domain protein Capture sequencing (MBDCap-seq) in human mammary epithelial cells (HMEC) originating from 4 healthy women (aged from 23 to 30 years old) after breast reduction mammoplasty.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 SRR1481501.sga HMEC|Bre67p2|H3K4me3 H3K4me3 GSM1421312
2 SRR1481503.sga HMEC|Bre98p2|H3K4me3 H3K4me3 GSM1421314
3 SRR1481504.sga HMEC|Bre98p4|H3K27me3 H3K27me3 GSM1421315
4 SRR1481505.sga HMEC|Bre98p4|H3K36me3 H3K36me3 GSM1421316
5 SRR1481506.sga HMEC|Bre98p5|H3K27ac H3K27ac GSM1421317
6 SRR1481507.sga HMEC|Bre98p5|Input input GSM1421318
7 SRR1481502.sga vHMEC|Bre67p7|H3K4me3 H3K4me3 GSM1421313
8 SRR1481508.sga vHMEC|Bre98p8|H3K4me3 H3K4me3 GSM1421319
9 SRR1481509.sga vHMEC|Bre98p9|H3K27ac H3K27ac GSM1421320
10 SRR1481510.sga vHMEC|Bre98p9|H3K27me3 H3K27me3 GSM1421321
11 SRR1481511.sga vHMEC|Bre98p9|H3K36me3 H3K36me3 GSM1421322
12 SRR1481512.sga vHMEC|Bre98p9|Input input GSM1421323

DNA-methylation:

Filename Description Feature GEO-ID
1 SRR1481514.sga HMEC|Bre12p3|MBDCap MBDCapSeq GSM1421325
2 SRR1481517.sga HMEC|Bre38p3|MBDCap MBDCapSeq GSM1421328
3 SRR1481520.sga HMEC|Bre67p2|MBDCap MBDCapSeq GSM1421331
4 SRR1481523.sga HMEC|Bre98p2|MBDCap MBDCapSeq GSM1421334
5 SRR1481515.sga vHMEC|Bre12p7|MBDCap MBDCapSeq GSM1421326
6 SRR1481513.sga vHMEC|Bre12p14|MBDCap MBDCapSeq GSM1421324
7 SRR1481518.sga vHMEC|Bre38p7|MBDCap MBDCapSeq GSM1421329
8 SRR1481516.sga vHMEC|Bre38p26|MBDCap MBDCapSeq GSM1421327
9 SRR1481521.sga vHMEC|Bre67p7|MBDCap MBDCapSeq GSM1421332
10 SRR1481519.sga vHMEC|Bre67p14|MBDCap MBDCapSeq GSM1421330
11 SRR1481524.sga vHMEC|Bre98p7|MBDCap MBDCapSeq GSM1421335
12 SRR1481522.sga vHMEC|Bre98p14|MBDCap MBDCapSeq GSM1421333

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: 14 Jan 2016