|
| Status |
Public on Aug 01, 2018 |
| Title |
163C1 |
| Sample type |
SRA |
| |
|
| Source name |
Urothelial Cancer
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
xenograft host: immunocompromised NGS mice
pdx model name: 163C
tumor type: Urothelial Cancer
|
| Growth protocol |
30 ml of peripheral blood was collected from patients with metastatic Urothelial Cancer prior to initiation of chemotherapy. Density gradient centrifugation was performed followed by isolation of circulating tumor cells through flow cytometry by depletion of CD45+ mononuclear cells and subsequent subcutaneous injection of CD45- cells into immunocompromised “NSG” mice. PDX that had undergone less than 5 passages were histologically confirmed and molecularly characterized by performing genome-wide transcriptome profiling using RNA-sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell suspensions of tissue sections of bladder CTC PDX models were obtained from CTC-PDX tumors by mechanically triturating the sample with a sterile scalper and forceps, without enzymatic digestion. RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with manufacturer's instructions. High-quality total RNA samples (RNA Integrity score >7.7 by Agilent Bioanalyzer) were subjected to poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer's protocol. The libraries were sequenced by HiSeq 2500 genome sequencer (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data files:
humanBetter_count.txt; humanOnly_count.txt; mouseBetter_count.txt; mouseOnly_count.txt
|
| Data processing |
Reads were first mapped to human and mouse genome separately using TopHat.
The Bamcmp algorithm was then used separate each read into human only, mouse only and both. The latter category was further categorized into reads aligning better to human or reads aligning better to mouse.
Genome_build: hg19,mm10
Supplementary_files_format_and_content: humanBetter_count.txt: reads mapped better to human genome; humanOnly_count.txt: reads only mapped to human genome; mouseBetter_count.txt: reads mapped better to mouse genome; mouseOnly_count.txt: reads only mapped to mouse genome;
|
| |
|
| Submission date |
Jun 22, 2018 |
| Last update date |
Aug 01, 2018 |
| Contact name |
Li Wang |
| Organization name |
Icahn school of medicine at Mount Sinai
|
| Street address |
1 Gustave L. Levy Pl
|
| City |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL22245 |
| Series (1) |
| GSE116159 |
RNA-seq profiling of patient-derived xenograft models in Urothelial Cancer |
|
| Relations |
| BioSample |
SAMN09470178 |
| SRA |
SRX4283514 |
