|
| Status |
Public on Jul 26, 2017 |
| Title |
1E61_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1
|
| Organism |
Homo sapiens |
| Characteristics |
group: CHD1_hom_del
genotype/variation: Hom_del
cell line: prostate carcinoma epithelial cell line 22Rv1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed by the UCLA Clinical Microarray Core (http://pathology.ucla.edu/cmc). For 22Rv1 cells RNA was extracted using the Quick RNA kit (Zymo Research).
RNA quality control, library preparation, and sequencing were performed by the UCLA Clinical Microarray Core (http://pathology.ucla.edu/cmc) and Tumor profiling Unit at the ICR (http://www.icr.ac.uk/our-research/our-research-centres/tumour-profiling-unit).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Processed data file: human_RNAseq_summary.txt
1E61
|
| Data processing |
The mice RNA-seq data were 100bp paired-end and mapped to mm9 using tophat (v2.0.13) utilizing bowtie with defaullt parameters. The 22Rv1 human cell line RNA-seq data were 100bp paired-end and mapped to Hg19 using TOPHAT2.
The FPKMs were calculated and normalized by cufflinks (v2.2.1).
The differentially transcribed gene analysis was carried out by cuffdiff.
For the 22Rv1 isogenic cell clones RNA-seq raw data were aligned to the human genome GRCh37.61 using TopHat (v2.0.7) with default parameters and transcripts were assembled based on Homo_sapiens.
GRCh37.61.gtf file. Relative expression level, represented as Fragments Per Kilobase of transcript per Million mapped reads (FPKM), were estimated by cufflinks v2.2.1 and normalized against total mapped reads per sample.
Genome_build: mm9 for mice, hg19 for humans
Supplementary_files_format_and_content: [.txt] tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Weilong Guo |
| E-mail(s) |
guoweilong@126.com
|
| Organization name |
Peking University
|
| Street address |
Intergrated Science Building
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE84610 |
CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair |
|
| Relations |
| BioSample |
SAMN05420177 |
| SRA |
SRX1961779 |
