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Sample GSM7688446 Query DataSets for GSM7688446
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

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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