Locke 2015, Epigenetic remodelling in early breast carcinogenesis

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.

• Raw data was downloaded from: GEO series: GSE58881
• Input file format: SRA

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

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:

HMEC: normal human mammary epithelial cells which have not yet escape senescence
vHMEC: variant HMEC population that have spontaneously escaped senescence and undergone partial carcinogenic transformation.
BreNpM: are the four isogenic HMEC/vHMEC lines where : N = donor id, pM = number of passages

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).

• Locke WJ, Zotenko E, Stirzaker C, Robinson MD, Hinshelwood RA, Stone A, Reddel RR, Huschtscha LI, Clark SJ
  Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Clin Epigenetics. 2015 May 1;7(1):52. doi: 10.1186/s13148-015-0086-0. eCollection 2015. 25960784
• GEO series GSE58881 Coordinated epigenetic remodelling occurs during early breast carcinogenesis [ChIP-seq & MBD-Seq].