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Series GSE90697 Query DataSets for GSE90697
Status Public on Sep 21, 2017
Title Organism-level analysis of vaccination reveals networks of protection across tissues
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To study the response of single lung and liver memory CD8+ T cells to reactivation, mice vaccinated subcutaneously with MVA (10^7 PFUs/mouse) were subsequently challenged intranasally with: (1) PBS; (2) WR (10^7 PFUs/mouse); or (3) Vaccinia virus-derived B8R20-27 peptide (20 µg/mouse). Sixteen hours after challenge, single-cell suspensions were generated from lung or liver and lymphocytes were enriched using Percoll density centrifugation prior to immunostaining and cell sorting. Single memory CD8+ T cells from lung and liver were profiled using plate-based or droplet-based single-cell RNA-seq.
Overall design Three datasets were generated from single memory CD8+ T cells isolated from lung or liver using plate-based (2,423 cells) or droplet-based (7,292) single-cell RNA-seq methods, which included: (i) 947 cells from lung of MVA-vaccinated mice challenged with PBS, WR or B8R20-27 peptide (plate-based – experiment 1); (ii) 1,476 cells from lung or liver of MVA-vaccinated mice challenged with PBS or WR (plate-based – experiment 2); and (iii) 7,292 cells from lung of MVA-vaccinated mice challenged with PBS or WR (droplet-based – experiment 3). Libraries from each experiment were sequenced as a single pool on an Illumina NextSeq500 sequencer.
Contributor(s) Chevrier N, Kadoki M
Citation(s) 28942919
Submission date Nov 30, 2016
Last update date May 15, 2019
Contact name Nicolas Chevrier
Organization name The University of Chicago
Department Pritzker School of Molecular Engineering
Lab Nicolas Chevrier
Street address 5640 South Ellis Avenue
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (11)
GSM2594420 Lung_PBS_plateBased_exp1
GSM2594421 Lung_WR_plateBased_exp1
GSM2594422 Lung_B8R_plateBased_exp1
BioProject PRJNA355404
SRA SRP094109

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE90697_Lung_CD8_dropletBased_exp3.txt.gz 31.5 Mb (ftp)(http) TXT
GSE90697_Lung_CD8_plateBased_exp1.txt.gz 838.3 Kb (ftp)(http) TXT
GSE90697_Lung_Liver_CD8_plateBased_exp2.txt.gz 1.2 Mb (ftp)(http) TXT
GSE90697_README_demultiplex.txt 269.4 Kb (ftp)(http) TXT
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