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Sample GSM7350188 Query DataSets for GSM7350188
Status Public on Apr 22, 2024
Title PC3 cells, siNC, ChIP-JUN
Sample type SRA
Source name PC3
Organism Homo sapiens
Characteristics cell line: PC3
cell type: Prostate cancer cell line
chip antibody: anti-JUN
treatment: Negative control knockdown
Treatment protocol PC3,NCI-H660 cells were treated with vehicle versus ORY-1001, or C12 for 4hrs
Growth protocol PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. NCI-H660 cells were cultured in RPMI-1640 base medium supplemented with 5% FBS, 10nM β-estradiol, 10nM hydrocortisone, and 1% Insulin-Transferrin-Selenium.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 2000
Description PC3, JUN, CST
Data processing The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.17-r1188) with aln and samse or sampe sub-commands.
Samtools (version 1.9) was used to convert sam files to bam format.
MACS2 (version 2.1.4) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 357).
Assembly: hg19
Supplementary files format and content: bigWig, bed
Submission date May 15, 2023
Last update date Apr 22, 2024
Contact name Zifeng Wang
Phone 6174709887
Organization name UMASS Boston
Department CPCT
Lab Changmeng Cai
Street address 100 Morrissey Blvd, ISC/4610
City Boston
State/province Massachusetts
ZIP/Postal code 02125
Country USA
Platform ID GPL30173
Series (2)
GSE232552 FOXA2/AP-1 drives prostate cancer lineage plasticity [ChIP-seq]
GSE232555 FOXA2/AP-1 drives prostate cancer lineage plasticity
BioSample SAMN35099526
SRA SRX20355964

Supplementary file Size Download File type/resource 174.0 Mb (ftp)(http) BW
GSM7350188_PC3_siNC_ChIP_JUN_peaks.bed.gz 328.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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