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| Status |
Public on May 20, 2016 |
| Title |
NTC R1881 2 AR |
| Sample type |
SRA |
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| Source name |
cell line VCaP
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| Organism |
Homo sapiens |
| Characteristics |
shRNA: PRMT5 NTC
chip antibody: AR
treatment: R1881
cell line: VCaP
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| Treatment protocol |
24h ligand as indicated for each sample
|
| Growth protocol |
DMEM, Charcol Dextran stripped FBS for hormone depletion(2days), Doxycycline for shRNA construct induction (5days)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP protocol - Purification using Magio beads
Kapa HTP library preparation kit on a Sciclone NGS workstation using MagBio beads
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ChIP DNA
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| Data processing |
BWA version 0.7.4-r385, aln parameters -q 5 -l 32 -k 2 -t 4
MACS2 version 2.1.0.20140616, callpeak --SPMR -B -q 0.01 --keep-dup 1
cat , all AR ChIPseq summit files
bedtools v2.20.1 slop -b 200, all AR ChIPseq summit files
bedtools v2.20.1 merge -d 1 -c 4 union AR ChIPseq summit file
Qlucore Omics Explorerer 3.1(19) - Generating summary Matrix file using union AR ChIPseq Peakfile, counting reads falling withing Peak features, Normalization according to Omics Explorer
Genome_build: hg19
Supplementary_files_format_and_content: raw data, pass filter Illumina NextSeq500 fastq files. Summit files, bed format Macs2 output, ChIPseq summits
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| Submission date |
Mar 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Westerling |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana Farber Cancer institute
|
| Department |
Medical Oncology
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| Lab |
Myles Brown
|
| Street address |
450 Brookline Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE79128 |
AR and ERG ChIP-seq in presence or absence of PRMT5 |
|
| Relations |
| BioSample |
SAMN04546549 |
| SRA |
SRX1629240 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2086298_NTC_R1881_2_AR.summit.bed.gz |
108.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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