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Sample GSM1656411 Query DataSets for GSM1656411
Status Public on Apr 14, 2015
Title input_ChIPSeq_abl
Sample type SRA
 
Source name prostate cancer cells
Organism Homo sapiens
Characteristics cell line: LNCaP-abl
cell type: androgen-independent prostate cancer cells
passages: 61-64
chip antibodies: none
Treatment protocol For the purpose of ChIP experiments, the cells were kept in androgen-depleted medium for 3 days before the cells were collected.
Growth protocol LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies. Libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 system following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Basecalls performed using CASAVA 1.6.0
ChIP-Seq reads are aligned to hg19 using Bowtie with default configurations, only uniqly mapped reads are kept
Redundant reads (reads mapped to exactly the same location) are removed
Peaks are called using MACS2 2.0.9
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are generated using MACS2+bedGraphToBigWig
 
Submission date Apr 13, 2015
Last update date May 15, 2019
Contact name Kexin Xu
E-mail(s) kxuthscsa@gmail.com
Organization name UT Health Science Center at San Antonio
Department Molecular Medicine
Street address 7703 Floyd Curl, MC 8257
City San Antonio
State/province TX
ZIP/Postal code 78229
Country USA
 
Platform ID GPL18573
Series (1)
GSE67809 Genome-wide chromatin binding of transcription factor E2F1 in castration resistant prostate cancer (CRPC) cells
Relations
BioSample SAMN03481182
SRA SRX992663

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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