|
| Status |
Public on Jan 01, 2024 |
| Title |
UPFL6 |
| 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 |
SAMN31572424 |
| SRA |
SRX18120715 |
