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| Status |
Public on Dec 05, 2013 |
| Title |
poor outcome_3_H3K4me3 |
| Sample type |
SRA |
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| Source name |
breast carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast tumor
procedure: ChIP-seq
chip antibody: ab8580 (Abcam)
aromatase inhibitor treatment outcome: poor
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| Treatment protocol |
primary tumor tissue was cryosectioned, 30x 30um sections were used
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Sep 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wilbert Zwart |
| Organization name |
NKI
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| 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 |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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