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Sample GSM1917733 Query DataSets for GSM1917733
Status Public on Oct 27, 2015
Title Input T2E 1
Sample type SRA
 
Source name Pc3 immortalized cells
Organism Homo sapiens
Characteristics cell line type: Pc3 Prostate Cancer Cell Line
antibody: none
treatment: 30 µm MnTE-2PyP for 24 hours
Treatment protocol PC3 cells were treated withand without 30 µm MnTE-2PyP for 24 hours, then exposed to 20 Gy of radiation. One hour after irradiation, the cells were harvested and fixed with 1% methanol-free formaldahyde.
Growth protocol PC3 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). PC3 cells were cultured in RPMI 1640 media containing L-glutamine, 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. All cell lines were maintained at 37°C and in 95% air and 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Chromatin was sheared using the isothermal Covaris S2 to produce approximately 100-300bp fragments for Ion Proton ChIP-seq. DNA-protein complexes were immunoprecipitated with an anti-p300 ChIP-grade antibody (Abcam #54984), captured by magnetic beads, cross-links reversed, and the genomic DNA purified (Invitrogen Magnify ChIP Kit #49-2024).
Libraries were made according to the instructions using the Ion Xpress Plus Fragment Library Kit- 4471269
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Ion Torrent Proton
 
Data processing ChIP-seq sequencing reads were aligned to the human reference genome using the Ion Torrent Suite software, version 4.0.2 and version 4.4
Peak-calling from aligned reads will be performed using the Model-based Analysis for ChIP-Sequencing (MACS2) software (Zhang, 2008), comparing p300 IPs to their respective total input controls. Peak significance was determined with a false discovery rate (FDR) cutoff of 0.001.
Peaks found by ChIP-seq will be associated with the nearest gene by genomic location, using both the RefSeq, refGene, and UCSC known gene models. A gene lists based on closest called peaks was generated.
Genome_build: HG19
Supplementary_files_format_and_content: peak.bed files were generated using MACS2 as described above
 
Submission date Oct 26, 2015
Last update date May 15, 2019
Contact name Brian Patrick OConnor
E-mail(s) oconnorb@njhealth.org
Organization name National Jewish Health
Department Center for Genes, Environment and Health
Lab OConnor
Street address 1400 Jackson St
City Denver
State/province Colorado
ZIP/Postal code 80206
Country USA
 
Platform ID GPL17303
Series (1)
GSE74351 P300 ChIP-Seq analysis of PC3 cells treated with MnTE-2-PyP or not 24 hours prior to irradiation of 20 Gy.
Relations
BioSample SAMN04215492
SRA SRX1382439

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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