|
Status |
Public on Mar 19, 2018 |
Title |
Bladder |
Sample type |
SRA |
|
|
Source name |
Bladder
|
Organism |
Mus musculus |
Characteristics |
tissue: Bladder age: 3 months
|
Extracted molecule |
total RNA |
Extraction protocol |
single-cell sorting in 96-well plates followed by cDNA preparation using Smart-seq2 Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
single cell
|
Data processing |
Sequences from the NovaSeq were demultiplexed using bcl2fastq version 2.19.0.316. Reads were aligned using to a copy of the mm10 genome augmented with ERCC sequences, using STAR version 2.5.2b STAR options are listed below --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField in Genome_build: mm10 Supplementary_files_format_and_content: comma-separated-value files with raw read counts for each sample
|
|
|
Submission date |
Jan 29, 2018 |
Last update date |
May 14, 2019 |
Contact name |
Angela Oliveira Pisco |
E-mail(s) |
angela.pisco@czbiohub.org
|
Organization name |
CZ Biohub
|
Department |
Data Sciences
|
Street address |
499 Illinois St
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94103 |
Country |
USA |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE109774 |
Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution |
GSE132042 |
Tabula Muris |
|
Relations |
BioSample |
SAMN08428438 |
SRA |
SRX3607041 |