|
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 |
E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
|
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 |
|
Relations |
BioSample |
SAMN18142680 |
SRA |
SRX10240706 |