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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
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]
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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