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Sample GSM7764594 Query DataSets for GSM7764594
Status Public on Sep 06, 2023
Title mouse CD8, 30hr, Transcriptome
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: CD8+ T cells
genotype: WT
time: 30 hr
treatment: 5 different pMHC conditions, or rested
Extracted molecule polyA RNA
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
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model NextSeq 2000
 
Description 10x Genomics
Transcriptome
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
 
Submission date Sep 06, 2023
Last update date Sep 06, 2023
Contact name Hao Yuan Kueh
E-mail(s) kueh@uw.edu
Organization name University of Washington
Department Bioengineering
Lab Kueh Lab
Street address 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
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
Relations
BioSample SAMN37305958
SRA SRX21652454

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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