|
| Status |
Public on May 21, 2013 |
| Title |
PA1 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured ovarian cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PA1
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 |
| |
|
| 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 |
SRX254234 |
| BioSample |
SAMN01985706 |
