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Series GSE67427 Query DataSets for GSE67427
Status Public on Mar 31, 2015
Title Mycobacterial infection induces a specific human innate immune response
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The innate immune system provides the first response to pathogen infection and orchestrates the activation of the adaptive immune system. Though a large component of the innate immune response is common to all infections, pathogen-specific innate immune responses have been documented as well. The innate immune response is thought to be especially critical for fighting infection with Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB). While TB can be a deadly disease, only 5-10% of individuals infected with MTB develop active disease, and this inter-individual variation is, at least partly, heritable. Studies of inter-individual variation in the innate immune response to MTB infection may therefore shed light on the genetic basis for variation in susceptibility to TB. Yet, to date, we still do not know which properties of the innate immune response are specific to MTB infection and which represent a general response to pathogen infection. To begin addressing this gap, we infected macrophages with eight different bacterial pathogens, including different MTB strains and related mycobacteria, and studied the transcriptional response to infection. We found that although the gene expression changes were largely consistent across the bacterial infection treatments, we were able to identify a novel subset of genes whose regulation was affected specifically by infection with mycobacteria. Genetic variants that are associated with regulatory differences in these genes should be considered candidate loci for explaining inter-individual susceptibility TB.
 
Overall design RNA-seq of monocyte-derived macrophages isolated from 6 healthy European males at 4, 18, and 48 hours post-infection with the following 8 bacteria: Mycobacterium tuberculosis (MTB) H37Rv, Mycobacterium tuberculosis GC1237, MTB GC1237, bacillus Calmette-Guérin (BCG), Mycobacterium smegmatis, Yersinia pseudotuberculosis, Salmonella typhimurium, and Staphylococcus epidermidis. table-s1.txt is a tab-delimited text file that contains the batch-corrected log2 counts per million for each of the 156 samples, as well as the Ensembl gene ID and gene name.

BCG = bacillus Calmette-Guérin
GC = Mycobacterium tuberculosis GC1237
Rv = Mycobacterium tuberculosis (MTB) H37Rv
Rv+ = heat-inactivated MTB H37Rv
Salm = Salmonella typhimurium
Smeg = Mycobacterium smegmatis
Staph = Staphylococcus epidermidis
Yers = Yersinia pseudotuberculosis
Web link https://bitbucket.org/jdblischak/tb
 
Contributor(s) Blischak JD, Tailleux L, Mitrano A, Barreiro LB, Gilad Y
Citation(s) 26586179
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AI087658 Mapping eQTLs that affect susceptibility to Tuberculosis UNIVERSITY OF CHICAGO GILAD
T32 GM007197 GENETICS AND REGULATION (NRSA): Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation: Genetics and Regulation UNIVERSITY OF CHICAGO LUCIA B. B ROTHMAN-DENES
Submission date Mar 30, 2015
Last update date May 15, 2019
Contact name John D Blischak
Organization name University of Chicago
Department Human Genetics
Lab Gilad
Street address 920 E. 58th Street, CLSC 317
City Chicago
State/province IL
ZIP/Postal code 60615
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (156)
GSM1646957 M372-none-4
GSM1646958 M375-Smeg-48
GSM1646959 M373-GC-18
Relations
BioProject PRJNA279959
SRA SRP056733

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE67427_table-s1.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data is available on Series record
Raw data are available in SRA

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