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Sample GSM8015523 Query DataSets for GSM8015523
Status Public on Apr 22, 2024
Title PC3 cells,vehicle, ChIP-FOXA2
Sample type SRA
 
Source name PC3
Organism Homo sapiens
Characteristics cell line: PC3
cell type: Prostate cancer cell line
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.
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) or Qiagen Qiaseq UltraLow Input Library Kit
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
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 Jan 12, 2024
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 GPL18573
Series (2)
GSE232552 FOXA2/AP-1 drives prostate cancer lineage plasticity [ChIP-seq]
GSE232555 FOXA2/AP-1 drives prostate cancer lineage plasticity
Relations
BioSample SAMN39420237
SRA SRX23182066

Supplementary file Size Download File type/resource
GSM8015523_ab256493_PC3_Rep1_21-01622_R1_peaks.bed.gz 859.8 Kb (ftp)(http) BED
GSM8015523_ab256493_PC3_Rep1_21-01622_R1_treat_pileup.bw 223.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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