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Sample GSM1003729 Query DataSets for GSM1003729
Status Public on Dec 05, 2013
Title poor outcome_3_H3K4me3
Sample type SRA
 
Source name breast carcinoma
Organism Homo sapiens
Characteristics tissue: primary breast tumor
procedure: ChIP-seq
chip antibody: ab8580 (Abcam)
aromatase inhibitor treatment outcome: poor
Treatment protocol primary tumor tissue was cryosectioned, 30x 30um sections were used
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nucle.Lysate was split into 3 equal volumes and for each ChIP (ER, H3K4me3, H3K27me3) protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Sequence data was generated and demultiplexed using the Illumina pipeline
Reads were aligned to hg19 with BWA version 0.5.10 using the default parameters
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) version 1.4.1. A p-value cutoff 1e-7 was used.
Genome_build: hg19
 
Submission date Sep 13, 2012
Last update date May 15, 2019
Contact name Wilbert Zwart
Organization name NKI
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platform ID GPL11154
Series (1)
GSE40867 Global mapping of estrogen receptor and histone modifications in breast tumor samples uncovers distinct patterns for aromatase inhibitor resistance
Relations
SRA SRX186819
BioSample SAMN01174241

Supplementary file Size Download File type/resource
GSM1003729_macs_wz89_vs_wz_036_peaks-chr.bed.gz 386.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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