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Sample GSM1104039 Query DataSets for GSM1104039
Status Public on May 21, 2013
Title OVCA433_3
Sample type SRA
Source name Cultured ovarian cancer cell line
Organism Homo sapiens
Characteristics cell line: OVCA433
cell type: ovarian cancer cells
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was harvested from the resulting cells by PureLink Genomic DNA kits (#K1820-01, Invitrogen)
Amplified DNA (20 ng) from PCR was used to construct a sequencing library using a ChIP-Seq sample preparation kit (#IP-102-1001, Illumina, San Diego, CA). The two sample-multiplexing sequencing method was used individually, with multiplexing index 6 and index 12 primers for each sample, (Illumina, #PE-400-1001).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer IIx
Description replicate
Data processing library strategy: DNA-seq
Basecalls performed using CASAVA version 1.6
DNA-seq reads were aligned to the shRNA TRC1.0 library using Bowtie version0.12.7 with options --solexa1.3-quals –n 0 –l 5 -v 0 -k 1 -m 1 --best –strata -y –nomaqround
Mapped reads are counted for each shRNA hairpins
Genome_build: shRNA library TRC1.0 (
Supplementary_files_format_and_content: tab-delimited text files include shRNA counts for each Sample.
Submission date Mar 22, 2013
Last update date May 15, 2019
Contact name Tuan Zea Tan
Organization name National University of Singapore
Department Cancer Science Institute Singapore
Street address 14 Medical Drive, #11-01, Singapore
City Singapore
ZIP/Postal code 117599
Country Singapore
Platform ID GPL10999
Series (1)
GSE45420 DNAseq data from human ovarian carcinoma cell lines subjected to shRNA TRC1.0 library
SRA SRX254245
BioSample SAMN01985717

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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