NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7828302 Query DataSets for GSM7828302
Status Public on Dec 27, 2023
Title FBC: CD45- lymph node cells from D5 Aire WT/KO mice, W2 Aire WT/KO mice, W5 Aire WT/KO mice
Sample type SRA
 
Source name LN
Organism Mus musculus
Characteristics tissue: LN
cell type: CD45- immune cells
strain: Aire.B6
Sex: Female
Extracted molecule total RNA
Extraction protocol Cells were released by digestion in Collagenase P, Dispase and DNaseI followed by filtering and washed in RPMI containing 5% fetal calf serum (FCS). CD45+ and CD45- cells were purified by fluorescence-activated cell sorting. Single cells were then sent to the Broad Institute Genomics Platform, which performed encapsulation following 10x Genomics protocols.
10x Genomics library prep, 3' v3 chemistry
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model HiSeq X Ten
 
Description 6 samples (3 AireWT and 3 AireKO CD45- LN cells) were hashed together into a single 10X scRNA-seq run
Data processing Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics).
Hash-by-cell matrices were computed using CITE-seq-count.
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Oct 05, 2023
Last update date Dec 27, 2023
Contact name CBDM Lab
E-mail(s) cbdm@hms.harvard.edu
Phone 617-432-7747
Organization name Harvard Medical School
Department Microbiology and Immunobiology
Lab CBDM
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL21273
Series (2)
GSE244742 Lymph Node Stromal Cell Responses to Perinatal T Cell Waves, A Temporal Atlas [scRNA-Seq]
GSE244743 Lymph Node Stromal Cell Responses to Perinatal T Cell Waves, A Temporal Atlas
Relations
BioSample SAMN37695136
SRA SRX22001499

Supplementary file Size Download File type/resource
GSM7828302_FBC_TJ_E4_barcodes.tsv.gz 360.8 Kb (ftp)(http) TSV
GSM7828302_FBC_TJ_E4_features.tsv.gz 144 b (ftp)(http) TSV
GSM7828302_FBC_TJ_E4_matrix.mtx.gz 943.6 Kb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap