Jansen 2013, H3K4me3, H3K27me3 and ERa in ER+ patient breast tumours.

Description

ChIP-seq against H3K4me3, H3K27me3 and ERα in primary tumors from selected ER-positive breast cancer patients from a bigger cohort from Belgium and the Netherlands, see (Ramirez-Ardila et al. 2012, PMID 23592373).

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1003708.sga good-1|ER ER GSM1003708
2 GSM1003709.sga good-1|H3K4me3 H3K4me3 GSM1003709
3 GSM1003710.sga good-1|good|H3K27me3 H3K27me3 GSM1003710
4 GSM1003711.sga good-2|ER ER GSM1003711
5 GSM1003712.sga good-2|H3K4me3 H3K4me3 GSM1003712
6 GSM1003713.sga good-2|H3K27me3 H3K27me3 GSM1003713
7 GSM1003714.sga good-3|ER ER GSM1003714
8 GSM1003715.sga good-3|H3K4me3 H3K4me3 GSM1003715
9 GSM1003716.sga good-3|H3K27me3 H3K27me3 GSM1003716
10 GSM1003717.sga good-4|ER ER GSM1003717
11 GSM1003718.sga good-4|H3K4me3 H3K4me3 GSM1003718
12 GSM1003719.sga good-4|H3K27me3 H3K27me3 GSM1003719
13 GSM1003720.sga good-5|ER ER GSM1003720
14 GSM1003721.sga good-5|H3K4me3 H3K4me3 GSM1003721
15 GSM1003722.sga good-5|H3K27me3 H3K27me3 GSM1003722
16 GSM1003723.sga poor-1|ER ER GSM1003723
17 GSM1003724.sga poor-1|H3K4me3 H3K4me3 GSM1003724
18 GSM1003725.sga poor-1|H3K27me3 H3K27me3 GSM1003725
19 GSM1003726.sga poor-2|ER ER GSM1003726
20 GSM1003727.sga poor-2|H3K27me3 H3K27me3 GSM1003727
21 GSM1003728.sga poor-3|ER ER GSM1003728
22 GSM1003729.sga poor-3|H3K4me3 H3K4me3 GSM1003729
23 GSM1003730.sga poor-3|H3K27me3 H3K27me3 GSM1003730
24 GSM1003731.sga poor-4|ER ER GSM1003731
25 GSM1003732.sga poor-4|H3K4me3 H3K4me3 GSM1003732
26 GSM1003733.sga poor-4|H3K27me3 H3K27me3 GSM1003733
27 GSM1003734.sga poor-5|ER ER GSM1003734
28 GSM1003735.sga poor-5|H3K4me3 H3K4me3 GSM1003735
29 GSM1003736.sga poor-5|H3K27me3 H3K27me3 GSM1003736
30 GSM1003737.sga poor-6|ER ER GSM1003737
31 GSM1003738.sga poor-6|H3K4me3 H3K4me3 GSM1003738
32 GSM1003739.sga poor-6|H3K27me3 H3K27me3 GSM1003739
33 GSM1003740.sga poor-7|ER ER GSM1003740
34 GSM1003741.sga poor-7|H3K4me3 H3K4me3 GSM1003741
35 GSM1003742.sga poor-7|H3K27me3 H3K27me3 GSM1003742
36 GSM1003743.sga mixed|Input Input GSM1003743

ChIP-seq peaks files:

Filename Description Feature GEO-ID
1 GSM1003708_peaks.sga good-1|ER_peaks ER_P GSM1003708
2 GSM1003711_peaks.sga good-2|ER_peaks ER_P GSM1003711
3 GSM1003714_peaks.sga good-3|ER_peaks ER_P GSM1003714
4 GSM1003717_peaks.sga good-4|ER_peaks ER_P GSM1003717
5 GSM1003720_peaks.sga good-5|ER_peaks ER_P GSM1003720
6 GSM1003723_peaks.sga poor-1|ER_peaks ER_P GSM1003723
7 GSM1003726_peaks.sga poor-2|ER_peaks ER_P GSM1003726
8 GSM1003728_peaks.sga poor-3|ER_peaks ER_P GSM1003728
9 GSM1003731_peaks.sga poor-4|ER_peaks ER_P GSM1003731
10 GSM1003734_peaks.sga poor-5|ER_peaks ER_P GSM1003734
11 GSM1003737_peaks.sga poor-6|ER_peaks ER_P GSM1003737
12 GSM1003740_peaks.sga poor-7|ER_peaks ER_P GSM1003740

Notes on samples nomenclature

Patients were treated with aromatase inhibtors for metastatic disease and classified as 'good' and 'poor' based on the outcome of the treatment. 'Poor' outcome patients were defined as patients with a time to progression (TTP) < 12 months, whereas 'good' outcome patients were defined as patients with a TTP > 24 months.

Mixed input: negative control (input chromatin) done with a mixture of tissue from all tumor samples.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the 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).
Conversion of author-supplied peak files into SGA and FPS format was also done with ChIP-Seq v. 1.5.2.

References

Last update: 4 May 2016