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Status |
Public on Sep 06, 2023 |
Title |
mouse CD8, 30hr, HashTagOligo |
Sample type |
SRA |
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Source name |
Spleen
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Organism |
Mus musculus |
Characteristics |
tissue: Spleen cell type: CD8+ T cells genotype: WT time: 30 hr treatment: 5 different pMHC conditions, or rested
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Extracted molecule |
protein |
Extraction protocol |
Following 30 hrs of stimulation, cells were stained with one of six hashtag (HTO) antibodies (1 ug HTO per sample) for 30 min at 4oC. 22k live cells (4k from each pMHC condition + 2k rested cells) were flow sorted using propidium iodide (Alfa Aesar, Cat # J66584). Single cell library preparation was done with the 10x Genomics platform, loading all 22k cells into a single lane. Libraries were diluted to 2nM using Agilent Tapestation D1000 HS and loaded onto two NextSeq 2000 P2 100-cycle kits using the following conditions: read 1: 28 cycles; index 1: 8 cycles; read 2: 92 cycles. scRNA-seq + Hash Tag Oligos
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Library strategy |
OTHER |
Library source |
other |
Library selection |
other |
Instrument model |
NextSeq 2000 |
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Description |
10x Genomics HTO
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Data processing |
Data was converted to fastq using bcl2fastq. Cellranger (version 6.0.1, 10x Genomics) was used for transcriptome- (337M reads) and HTO- (161M reads) level unique molecular identifier (UMI) and cell demultiplexing, and for aligning the transcriptome to the GRCm38/mm10 reference genome. Doublets and cells with > 7.5% mitochondrial reads were removed. Quality control, pre-processing, dimensionality reduction, and UMAP visualization were done with Monocle3 (v 1.2.9) in R Assembly: GRCm38/mm10 Supplementary files format and content: Tab-separated values files and matrix files
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Submission date |
Sep 06, 2023 |
Last update date |
Sep 06, 2023 |
Contact name |
Hao Yuan Kueh |
E-mail(s) |
kueh@uw.edu
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Organization name |
University of Washington
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Department |
Bioengineering
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Lab |
Kueh Lab
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Street address |
3720 15th Ave NE
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
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Platform ID |
GPL30172 |
Series (2) |
GSE242494 |
Antigen perception in T cells by long-term Erk and NFAT signaling dynamics [scRNAseq] |
GSE242495 |
Antigen perception in T cells by long-term Erk and NFAT signaling dynamics |
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Relations |
BioSample |
SAMN37305957 |
SRA |
SRX21652455 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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