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Sample GSM3211544 Query DataSets for GSM3211544
Status Public on Aug 01, 2018
Title 173C3
Sample type SRA
Source name Urothelial Cancer
Organisms Homo sapiens; Mus musculus
Characteristics xenograft host: immunocompromised NGS mice
pdx model name: 173C
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
BioSample SAMN09470188
SRA SRX4283519

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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