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Sample GSM7350185 Query DataSets for GSM7350185
Status Public on Apr 22, 2024
Title PC3 cells, siFOXA2, ChIP-FOSL1
Sample type SRA
 
Source name PC3
Organism Homo sapiens
Characteristics cell line: PC3
cell type: Prostate cancer cell line
chip antibody: anti-FOSL1
treatment: FOXA2 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, FOSL1, 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
E-mail(s) wzifeng8@gmail.com
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
Relations
BioSample SAMN35099529
SRA SRX20355961

Supplementary file Size Download File type/resource
GSM7350185_PC3_siFOXA2_ChIP_FOSL1.bed.gz 21.1 Kb (ftp)(http) BED
GSM7350185_PC3_siFOXA2_ChIP_FOSL1_treat.bw 16.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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