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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 |
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 Selector |
| Raw data are available in SRA |
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