|
Status |
Public on Aug 10, 2023 |
Title |
mouse FADS sorted PBMCs |
Sample type |
SRA |
|
|
Source name |
mouse splenocytes, frozen
|
Organism |
Mus musculus |
Characteristics |
tissue: mouse splenocytes, frozen cell line: C57BL/6 cell type: splenocytes genotype: WT treatment: thawed, treated with FC block, stained with fluorescently-labelled antibodies and sequenced using spinDrop
|
Extracted molecule |
total RNA |
Extraction protocol |
Live cells were stained with PE-labelled antibodies or Calcein-AM Bead barcoding: indrop v3 protocol, encapsulation: spinDrop protocol, downstream library preparation: inDrop v3 protocol inDrop v3 protocol
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
RNA spindrop FADS_PBMC_matrix.csv
|
Data processing |
FastQC quality control Pheniqs for demultiplexing zUMIs to generate gene expression matrices using mouse and human references with Ensembl v99 annotations Seurat v3 for data integration and analysis Assembly: GRCm38 genome (Ensembl 99) and GRCh38 genome (Ensembl 99) Supplementary files format and content: UMI quantified reads mapping to intronic and exonic regions. Downsampled to 20,000 reads per cell when indicated in the file header.
|
|
|
Submission date |
Aug 07, 2023 |
Last update date |
Aug 10, 2023 |
Contact name |
Florian Hollfelder |
E-mail(s) |
fh111@cam.ac.uk
|
Organization name |
University of Cambridge
|
Street address |
80 tennis court road
|
City |
Cambridge |
ZIP/Postal code |
CB21GA |
Country |
United Kingdom |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE208156 |
spinDrop: a modular droplet microfluidic platform to maximise single-cell RNA sequencing information content |
|
Relations |
BioSample |
SAMN36871503 |
SRA |
SRX21278071 |