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Sample GSM4146953 Query DataSets for GSM4146953
Status Public on Nov 02, 2019
Title Non-SCCB8
Sample type SRA
 
Source name Clinical Non-SCCB sample
Organism Homo sapiens
Characteristics tissue: Non-SCCB (urothelial carcinoma)
sample type: Archived FFPE samples
Growth protocol For bladder-PARCB cell lines, cells were cultured in stem cell culture medium in regular tissue culture flask. The cells grow in suspension condition.
Extracted molecule total RNA
Extraction protocol For clinical samples, using Ambion RecoverAll kit (Thermofisher, #AM1975); For Bladder-PARCB cells, using Qiagen miRNeasy kit (Qiagen, #217004)
Human FFPE RNA-seq kit (Nugen, #0341-32)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Raw reads were mapped to hg38 human genome using TOIL
Transcripts were quantified by expectation-maximization (RSEM), TPM was calculated
Gene list was filtered for HUGO coding genes
Supplementary_files_format_and_content: TPM-HUGO-FFPE.txt: the TPM matrix for clinical samples; TPM-HUGO-Bladder-PARCB.txt: the TPM matrix for Bladder-PARCB cell lines
 
Submission date Nov 01, 2019
Last update date Nov 06, 2019
Contact name Liang Wang
E-mail(s) liangwang@mednet.ucla.edu
Organization name UCLA
Department MIMG
Lab Owen Witte
Street address 675 Charles E Young Dr
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL21290
Series (1)
GSE139822 RNA-seq data of small cell carcinoma of the bladder (SCCB) /urothelial carcinoma (Non-SCCB) clinical samples, and bladder-PARCB cell lines
Relations
BioSample SAMN13176404
SRA SRX7085318

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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