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Sample GSM6704993 Query DataSets for GSM6704993
Status Public on Jan 01, 2024
Title UPFL1
Sample type SRA
 
Source name bladder tumor
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bladder tumor
tissue type: primary UPFL tumor
treatment: untreated
Extracted molecule total RNA
Extraction protocol RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description bulk RNA
Data processing 75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
Illumina Novaseq_6000 for scRNAseq base calling
Transcript abundance estimates for cell were performed using cell ranger
Supplementary files format and content: Tab-delimited text files include Normalized count values for each sample
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples
Assembly: mm10
 
Submission date Nov 02, 2022
Last update date Jan 01, 2024
Contact name William Kim
E-mail(s) william_kim@med.unc.edu
Organization name UNC Chapel Hill
Department Lineberger Comprehensive Cancer Center
Street address 450 West Dr
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL19057
Series (1)
GSE217093 RNAseq and scRNAseq analysis of UPFL mouse tumors
Relations
BioSample SAMN31572429
SRA SRX18120710

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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