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| Status |
Public on Aug 19, 2022 |
| Title |
TCF7-GFP+_P14_T_cells |
| Sample type |
SRA |
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| Source name |
splenic_CD8+_T_cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+_T_cells
strain: C57BL/6
tissue: spleen
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| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x genomics)
Chromium Single Cell 3′ Library Construction Kit (10x genomics)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
scRNAseq
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| Data processing |
Cell Ranger (version 5.0.0; 10x Genomics) was used for demultiplexing and alignment (resulting in the bam file) as well as counting (resulting in the mtx and tsv files) using default parameters
velocyto (version 0.17.17) performed counting of spliced and unspliced RNA molecules (based on bam file) to create loom file
Python software package SCANPY (version 1.6) was used for downstream analysis
Cells were filtered out that express < 200 genes and >4500 genes, >20000 counts, > 15% mitochondrial genes. Genes were filtered out that were present in < 3 cells.
Cell cycle, percent mito and n_counts were regressed out
Assembly: mouse reference genome GRCm38
Supplementary files format and content: Output of the Cell Ranger Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized)
Supplementary files format and content: unnormalized and unfiltered loom-file, containing information about spliced and unspliced mRNA counts
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| Submission date |
Mar 31, 2022 |
| Last update date |
Aug 19, 2022 |
| Contact name |
Lorenz Kretschmer |
| E-mail(s) |
lorenz.kretschmer@tum.de
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| Organization name |
TU Munich
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| Department |
Institute for Medical Microbiology, Immunology and Hygiene
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| Lab |
Dr. Veit R. Buchholz
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| Street address |
Trogerstr. 30
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| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
81675 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE199839 |
c-Myb instructs both stemness and functional exhaustion of CD8+ T cells during chronic infection [scRNA-seq] |
| GSE205608 |
c-Myb instructs both stemness and functional exhaustion of CD8+ T cells during chronic infection |
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| Relations |
| BioSample |
SAMN27120738 |
| SRA |
SRX14684712 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5988328_TCF7_GFP+_spleen_barcodes.tsv.gz |
24.0 Kb |
(ftp)(http) |
TSV |
| GSM5988328_TCF7_GFP+_spleen_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM5988328_TCF7_GFP+_spleen_loom.loom.gz |
54.4 Mb |
(ftp)(http) |
LOOM |
| GSM5988328_TCF7_GFP+_spleen_matrix.mtx.gz |
30.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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