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| Status |
Public on Oct 27, 2015 |
| Title |
Input T2E 2 |
| Sample type |
SRA |
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| Source name |
Pc3 immortalized cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line type: Pc3 Prostate Cancer Cell Line
antibody: none
treatment: 30 µm MnTE-2PyP for 24 hours
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| 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.
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| 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.
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
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| 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
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| Submission date |
Oct 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Patrick OConnor |
| E-mail(s) |
oconnorb@njhealth.org
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| Organization name |
National Jewish Health
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| Department |
Center for Genes, Environment and Health
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| Lab |
OConnor
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| Street address |
1400 Jackson St
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| City |
Denver |
| State/province |
Colorado |
| ZIP/Postal code |
80206 |
| Country |
USA |
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| 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. |
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| Relations |
| BioSample |
SAMN04215493 |
| SRA |
SRX1382440 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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