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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 |
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Source name |
LN
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Organism |
Mus musculus |
Characteristics |
tissue: LN cell type: CD45+ immune cells strain: Aire.B6 Sex: Female
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Description |
6 samples (3 AireWT and 3 AireKO CD45+ LN cells) were hashed together into a single 10X scRNA-seq run
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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
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Submission date |
Oct 05, 2023 |
Last update date |
Dec 27, 2023 |
Contact name |
CBDM Lab |
E-mail(s) |
cbdm@hms.harvard.edu
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Phone |
617-432-7747
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Organization name |
Harvard Medical School
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Department |
Microbiology and Immunobiology
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Lab |
CBDM
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Street address |
77 Avenue Louis Pasteur
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02215 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN37695137 |
SRA |
SRX22001498 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7828301_FBC_TJ_E3_barcodes.tsv.gz |
361.7 Kb |
(ftp)(http) |
TSV |
GSM7828301_FBC_TJ_E3_features.tsv.gz |
144 b |
(ftp)(http) |
TSV |
GSM7828301_FBC_TJ_E3_matrix.mtx.gz |
936.8 Kb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
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