|
| Status |
Public on Mar 19, 2018 |
| Title |
Liver |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
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 |
SAMN08428463 |
| SRA |
SRX3607048 |
