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Series GSE87633 Query DataSets for GSE87633
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 Whole organs or CD8+ T cell populations sorted by FACS from tissues were isolated at various time points following vaccination with Vaccinia virus strain Modified Vaccinia Ankara (MVA; subcutaneously) and/or infection with strain Western Reserve (WR; intranasally). Total RNA was extracted from whole organs or sorted cell populations, RNA-seq libraries were prepared with a custom protocol, and sequenced at an average depth of ~5M/sample.
Overall design We compared three types of immune responses in vivo: (1) vaccinating (MVA only; 10^7 PFUs subcutaneously), (2) lethal (WR only; 10^7 PFUs intranasally), and (3) protective (MVA followed by WR challenge; same doses and routes as in 1 and 2, respectively). Overall, 6 datasets were generated from the following experiments and samples:
(i) Whole-tissue samples from MVA, WR, MVA+WR cohorts with WR challenge at day 7, 21 (Exp. 1), or 80 (Exp. 2) in wild-type mice;
(ii) Whole-tissue samples from MVA+WR at day 21 in wild-type versus knockout animals: Tcra-/- (Exp. 3), and Ifng-/-, Il22-/-, and Csf2-/- (Exp. 5);
(iii) Sorted CD8+ T cell populations profiled from tissues of MVA-vaccinated (day 21) and control mice with (Exp. 6) or without (Exp. 4) intravascular staining (anti-CD45-PE antibody) to distinguish parenchyma-associated from vasculature-associated cells.
Contributor(s) Chevrier N, Kadoki M
Citation(s) 28942919
Submission date Oct 05, 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 (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (737)
GSM2593669 BM__control_M1_exp1
GSM2593670 BM__control_M138_exp1
GSM2593671 BM__control_M139_exp1
BioProject PRJNA345545
SRA SRP090924

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE87633_raw_counts_exp1_day7_day21.txt.gz 9.9 Mb (ftp)(http) TXT
GSE87633_raw_counts_exp2_day21_day80.txt.gz 1.3 Mb (ftp)(http) TXT
GSE87633_raw_counts_exp3_TcraKO.txt.gz 873.0 Kb (ftp)(http) TXT
GSE87633_raw_counts_exp4_sortedCD8.txt.gz 731.4 Kb (ftp)(http) TXT
GSE87633_raw_counts_exp5_KOs.txt.gz 916.8 Kb (ftp)(http) TXT
GSE87633_raw_counts_exp6_IVstaining_sortedCD8.txt.gz 408.6 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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