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| Status |
Public on Mar 27, 2024 |
| Title |
ERa_BRCa_patient_3 |
| Sample type |
SRA |
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| Source name |
primary breast tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast tumor
disease state: breast cancer
individual: patient_3
chip antibody: Era (SX-543, Santa Cruz)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh frozen tumor material was cryosectioned, collected in Eppendorf tubes and stored at -80C until processing. An H&E slide was assessed by pathologist to confirm tumor cell content. For ChIP, tissue was thawed on ice and cross-linked in solution A (50 mM Hepes, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, pH = 7.4) containing 2 mM DSG (Sigma) and incubated at room temperature for 25 min while rotating. Next, formaldehyde was added to 1% final concentration and rotation was continued for 20 min. Reaction was quenched by 0.2 M glycine. Samples were pelleted, washed with cold PBS and tissue architecture was disrupted by a pellet pestle (Sigma) and subsequently sonicated (Diagenode PicoBioruptor). IP was performed by overnight incubation with 5 ug ER antibody (SC-543, Santa Cruz) to 50uL dynabeads (Invitrogen) in blocking buffer (5% BSA in PBS), then washed 10 times with RIPA (50 mM HEPES, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-DOC, pH = 7.6), washed in TBS, reverse cross-linked at 65C in Elution Buffer (50mM Tris, 10mM EDTA, 1% SDS) and DNA eluted.
ChIP DNA was prepared for Illumina multiplex-sequencing with 10 samples per lane and sequenced on Illumina HiSeq 2500 (Illumina) at 65bp single-end.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were aligned to the human genome build GRCh37 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis
Enrichment over input control was determined using both MACS2. Only peaks identified by both methods, and not overlapping with the ENCODE GRCh37/Hg19 blacklisted regions, were retained.
Deeptools bamCoverage was used to egnerate Reads-Per-Genomic-Contact (RPGC) normalized bigwig files.
Raw data vailable at EGA: EGAS50000000008
Assembly: Hg19/GRCh37
Supplementary files format and content: .bed, peaks
Supplementary files format and content: .bw, BigWig of RPGC normalized ChIP-seq signal
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| Submission date |
Oct 06, 2023 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Wilbert Zwart |
| E-mail(s) |
w.zwart@nki.nl
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| Organization name |
Netherlands Cancer Institute
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| Department |
Oncogenomics
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| Lab |
Hormone-dependent cancers
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| State/province |
Noord-Holland |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE244840 |
Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions [ChIP-seq] |
| GSE244845 |
Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7830651_ERa_BCa_patient_3.bed.gz |
44.1 Kb |
(ftp)(http) |
BED |
| GSM7830651_ERa_BRCa_patient_3_mapq20_mdup_RPGC.normalized_bs50.bw |
118.5 Mb |
(ftp)(http) |
BW |
| Raw data not provided for this record |
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