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Sample GSM5135522 Query DataSets for GSM5135522
Status Public on May 05, 2022
Title WT (F7)
Sample type SRA
Source name exhausted CD8 T cell
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: spleen
cell type: exhausted CD8 T cell
genotype: wild type
treatment: untreated
Treatment protocol B/6 Mice were infected with 2x10^6 IU LCMV clone13 after 2 times CD4 T cell depletion (d-2 and d0) with 300µg GK1.5 antibody. At the chronic infection phase (> d30), splenocytes were isolated and CD8+, PD-1+, Tim-3 low cells were sorted using FACS AriaIII. Treated mice were injected i.p. 200µg aPD-L1 antibody (clone 10F.9G2) 24h before sacrificing the mice. Cells were pooled form 4 mice per group.
Extracted molecule polyA RNA
Extraction protocol Mice were sacrificed and spleen isolated. Single cell suspnesion was created by grinding spleens though a filter. Afterwards, red blood cells were lysed with ACK-buffer for 4min. Splenocytes were staining with antibodies for 30min at 4 degrees and sorted for the desired population using FACS AriaIII.
CD8+, PD-1+, TIM-3 negative single-cells were sorted from the spleen of chronically infected mice using a FACSAria III (BD Biosciences), before being encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 for the WT untreated sample or v3 for WT sample treated with aPD-L1 (10x Genomics) following the detailed protocol provided by the manufacturer.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing The sequencing data was processed using CellRanger software (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
Submission date Mar 04, 2021
Last update date May 05, 2022
Contact name Antoine-Emmanuel Saliba
Phone +49-931-31-81341
Organization name Helmholtz Institute for RNA-based Infection Research
Street address Josef-Schneider-Straße 2 / D15
City Würzburg
ZIP/Postal code 97080
Country Germany
Platform ID GPL24247
Series (1)
GSE168282 cDC1 retain a niche for precursor exhausted T cells during chronic viral infection
BioSample SAMN18142680
SRA SRX10240706

Supplementary file Size Download File type/resource
GSM5135522_F7_filtered_gene_bc_matrices.tar.gz 16.7 Mb (ftp)(http) TAR
GSM5135522_F7_molecule_info.h5 176.3 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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