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Sample GSM7971837 Query DataSets for GSM7971837
Status Public on Jun 12, 2024
Title WT_Thymus_TCR [GA41205]
Sample type SRA
 
Source name thymus
Organism Mus musculus
Characteristics tissue: thymus
cell type: thymocyte
genotype: wild type
library type: TCR V(D)J segments
Treatment protocol Thymocyte were homoginized and enriched MR1-5-OP-RU tetramer positive T cells by MACS sorting.
Extracted molecule total RNA
Extraction protocol Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequencing was performed on NovaSeq 6000 platform in a 50+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence) - cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0 and refdata-gex-mm10-2020-A
Supplementary files format and content: mouse_Thymus_genematrix.csv : comma-delimited text files including UMI counts for each feature (gene or HTO) and cell (barcode) conbination
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the TCR clonotype information
 
Submission date Dec 12, 2023
Last update date Jun 12, 2024
Contact name Daisuke Motooka
E-mail(s) dry_team@ngs.gen-info.osaka-u.ac.jp
Organization name NGS core facility, Research Institute for Microbial Diseases, Osaka University
Street address 3-1, Yamadaoka
City Suita
State/province Osaka
ZIP/Postal code 5650871
Country Japan
 
Platform ID GPL24247
Series (1)
GSE204917 MR1 presents sulfated bile acid as a self antigen for MAIT cells [single-cell RNA-seq]
Relations
BioSample SAMN38792375
SRA SRX22870183

Supplementary file Size Download File type/resource
GSM7971837_airr_rearrangement.tsv.gz 20.0 Kb (ftp)(http) TSV
GSM7971837_clonotypes.csv.gz 1.5 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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