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Status |
Public on Dec 27, 2018 |
Title |
MCF7_H3K4me3_DSG |
Sample type |
SRA |
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Source name |
MCF7 cell line
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Organism |
Homo sapiens |
Characteristics |
chip antibody: H3K4me3 (Abcam; ab8580) patient id: MCF7_H3K4me3_DSG case/control: DSG
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Treatment protocol |
Surgical resections from Prostate, breast and endometrium tumors.
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Growth protocol |
fresh frozen material
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Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
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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 |
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline. Reads were aligned to the Human Reference Genome (Ensembl release 55: Homosapiens GRCh 37.55) using BWA9. Reads with a BWA alignment quality score less than 20 were removed. Genome_build: GRCh 37.55
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Submission date |
May 21, 2018 |
Last update date |
Dec 27, 2018 |
Contact name |
Abhishek Singh |
E-mail(s) |
abhisheksinghnl@gmail.com
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Organization name |
Netherlands Cancer Institute
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Street address |
Plesmanlaan
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City |
Amsterdam |
ZIP/Postal code |
1066CX |
Country |
Netherlands |
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Platform ID |
GPL16791 |
Series (1) |
GSE114737 |
Optimized ChIP-seq procedure facilitates hormone receptor profiling in human tumors |
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Relations |
BioSample |
SAMN09238289 |
SRA |
SRX4115997 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3149035_MCF7_H3K4me3_DSG.bed.gz |
148.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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