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Sample GSM7830651 Query DataSets for GSM7830651
Status Public on Mar 27, 2024
Title ERa_BRCa_patient_3
Sample type SRA
 
Source name primary breast tumor
Organism Homo sapiens
Characteristics tissue: primary breast tumor
disease state: breast cancer
individual: patient_3
chip antibody: Era (SX-543, Santa Cruz)
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Oct 06, 2023
Last update date Jun 03, 2024
Contact name Wilbert Zwart
E-mail(s) w.zwart@nki.nl
Organization name Netherlands Cancer Institute
Department Oncogenomics
Lab Zwart lab
Street address Plesmanlaan 121
City Amsterdam
State/province Noord-Holland
ZIP/Postal code 1066CX
Country Netherlands
 
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

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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