NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1104037 Query DataSets for GSM1104037
Status Public on May 21, 2013
Title HEYA8_2
Sample type SRA
 
Source name Cultured ovarian cancer cell line
Organism Homo sapiens
Characteristics cell line: HEYA8
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 (http://www.broadinstitute.org/rnai/trc/lib)
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
E-mail(s) csittz@nus.edu.sg
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
Relations
SRA SRX254243
BioSample SAMN01985715

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap