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| Status |
Public on Oct 03, 2018 |
| Title |
P433T_H3K4me3 |
| Sample type |
SRA |
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| Source name |
primary prostate cancer
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| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3 (Abcam, catalog# Ab8580, lot# GR240214-2)
patient id: P433T
case/control: Control
tissue: primary prostate cancer
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| Treatment protocol |
prostatectomy samples, labeled according to recurrence status (case/control/exclude)
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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 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peak calling over input control (mixed inputs) was performed using DFilter and MACS for AR, H3K27ac, H3K4me3 ChIP-seq samples. The peaks called by both peak callers were used for analysis.
H3K27me3 ChIP-seq peaks were called by genome segmentation using ChromHMM chosing the state with high H3K27me3 signal (binary data, no quantitative data)
Genome_build: hg19
Supplementary_files_format_and_content: bed
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| Submission date |
Oct 02, 2018 |
| Last update date |
Oct 03, 2018 |
| Contact name |
Suzan Stelloo |
| E-mail(s) |
Stelloo@science.ru.nl
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| Organization name |
Radboud University
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| Department |
Molecular Biology
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| Street address |
Geert Grooteplein Zuid 28
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| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE120738 |
Integrative epigenetic taxonomy of primary prostate cancer [ChIP-Seq] |
| GSE120742 |
Integrative epigenetic taxonomy of primary prostate cancer |
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| Relations |
| BioSample |
SAMN10160633 |
| SRA |
SRX4783228 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3409849_3753_75_wz1168_CCGACAAC_S75_L008.FILTERED20.macs_peaks.filtered.intersect.txt.gz |
314.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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