|
| Status |
Public on Apr 30, 2020 |
| Title |
tabula-muris-senis-facs |
| Sample type |
SRA |
| |
|
| Source name |
tabula_muris_senis_facs_raw_counts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy (mini and micro) Qiagen RNA isolation from homogenized tissue.
10X genomics and 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
tabula_muris_senis_facs_raw_counts
SmartSeq2 single-cell raw counts
|
| Data processing |
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316.
Reads were aligned using to the mm10plus genome using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data is available as h5ad and loom. Metadata is available from the h5ad or as separate csv.
|
| |
|
| Submission date |
Apr 29, 2020 |
| Last update date |
Apr 30, 2020 |
| 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) |
|
| Relations |
| BioSample |
SAMN14771164 |
