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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 20, 2011 |
| Title |
PC3 JUND |
| Sample type |
SRA |
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| Source name |
PC3_JUND
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| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
antibody: JUND(Santa Cruz Biotechnology, cat# sc-74, lot# C0310)
retroviral expression: None
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| Growth protocol |
Growth according to ATCC
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were constructed using the Illumina ChIP-seq kit following the included protocol
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
hg18
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| Data processing |
Software from the Useq package was used to identify peaks. ElandParser mapped sorted.txt files and SamParser mapped fastq files. FilterPointData was used to remove reads mapping to repeat regions included in the satellite repeat track from the UCSC genome browser. PeakShift finder was used to measure the shift in peak location between each DNA strand. Peak shifts were JunD:250, ETV1:100, ETS1:270, ERG:270, ETV4:260, GABPA:250. ScanSeqs used a sliding window of approximately twice the peak shift to score enrichment across the genome and adjusted reads by the peak shift to remove peak shift bias. Windows were 500 bp for all samples except ETV1 which was 250 bp. Enriched regions maker identified enriched regions. Significance was determined by calculating a bionomial P value for each window and controlled for multiple testing by calculating an empirical false discovery rate.
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| Submission date |
Jun 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Hollenhorst |
| E-mail(s) |
[email protected]
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| Organization name |
Indiana University
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| Street address |
1001 E Third St, Jordan Hall 104
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| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE29808 |
Oncogenic ETS proteins replace activated Ras/MAPK signaling in prostate cells. |
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| Relations |
| SRA |
SRX084522 |
| BioSample |
SAMN00672564 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM738818_JUND_PC3_2973_bed.txt.gz |
28.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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