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Series GSE49933 Query DataSets for GSE49933
Status Public on Mar 03, 2014
Title RNA-Seq global gene expression in lung tissue at ten time points during a 7-day time course of infection
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Hundreds of immune cell types work in coordination to maintain tissue homeostasis. Upon infection, dramatic changes occur with the localization, migration and proliferation of the immune cells to first alert the body of the danger, confine it to limit spreading, and finally extinguish the threat and bring the tissue back to homeostasis. Since current technologies can follow the dynamics of only a limited number of cell types, we have yet to grasp the full complexity of global in vivo cell dynamics in normal developmental processes and disease. Here we devise a computational method, digital cell quantification (DCQ), which combines genomewide gene expression data with an immune cell compendium to infer in vivo dynamical changes in the quantities of 213 immune cell subpopulations. DCQ was applied to study global immune cell dynamics in mice lungs at ten time points during a 7-day time course of flu infection. We find dramatic changes in quantities of 70 immune cell types, including various innate, adaptive and progenitor immune cells. We focus on the previously unreported dynamics of four immune dendritic cell subtypes, and suggest a specific role for CD103+CD11b- cDCs in early stages of disease and CD8+ pDC in late stages of flu infection.
Overall design To study pathogenesis of Influenza infection, C57BL/6 mice (5 weeks) were infected intranasally with 4x103 PFU of influenza PR8 virus. We measured using RNA-Seq global gene expression in lung tissue at ten time points during a 7-day time course of infection, two infected individuals in each time point and four un-infected individuals as control. The lung organ was removed and transferred immediately into RNA Latter solution (Invitrogen).
Contributor(s) Michal M, Irit G, Ido A
Citation(s) 24586061
Submission date Aug 16, 2013
Last update date May 15, 2019
Contact name Irit Gat-Viks
Organization name Tel-Aviv University
Department Department of Cell Research and Immunology
Street address Tel-Aviv
City Tel-Aviv
ZIP/Postal code 69978
Country Israel
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (23)
GSM1210255 strain B6 uninfected, repeat 1
GSM1210256 strain B6 uninfected, repeat 2
GSM1210257 strain B6 uninfected, repeat 3
This SubSeries is part of SuperSeries:
GSE49934 Flu infection
BioProject PRJNA215375
SRA SRP028868

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49933_RAW.tar 3.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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