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Series GSE156844 Query DataSets for GSE156844
Status Public on Oct 02, 2020
Title Type I interferome in human gut CD4 T cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Rationale: Humans encode 12 different IFNa proteins. All of them, except IFNa1 (only binds with IFNAR1), bind with IFNAR1 and IFNAR2 to activate their downstream functions. Currently in the field, it is still a debate whether there are qualitative difference between different IFNa subtypes or the differences are merely quantitative. The current study was set out to elucidate the question.
Methods: CD4 T cells purified from LPMCs from gut biopsies from 3 donors, subsequently were mock treated or with ISRE activity normalized IFNa1, IFNa2, IFNa5, IFNa8, IFNa14, or IFNb. RNAs were extracted from cells after 18 hrs of incubation. RNASeq libraries were generated using Lexogen Quant Seq 3’ mRNA-Seq library Prep Kit. RNASeq were performed on Illumina HiSeq 2500.
Results: An average of 11.4 million gene counts were identified for each donor/treatment. A total of 31,465 genes were mapped, and among them 1,981 genes were differentially expressed due to type I interferon treatments. Each of IFNa subtypes or IFNb has their specifically regulated genes.
Conclusion: There are qualitative differences between type I interferons.
 
Overall design Transcriptomic profiles of CD4 T cells treated with different Type I interferons.
 
Contributor(s) Guo K, Kibbie J, Gonzalez T, Santiago M
Citation(s)
  • Guo K, Shen G, Kibbie J, Gonzalez T et al. Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis. PLoS Pathog 2020 Oct;16(10):e1008986. PMID: 33064743
BioProject PRJNA558974
Submission date Aug 25, 2020
Last update date Jun 30, 2023
Contact name Kejun Guo
E-mail(s) Kejun.guo@cuanschutz.edu
Phone 3037245291
Organization name University of Colorado Anschutz Medical Campus
Department Division of Infectious Diseases
Street address 12700 E 19th Ave, Rm 11420D
City Aurora
State/province Colorado
ZIP/Postal code 80045
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (21)
GSM4745313 g356_Mock
GSM4745314 g392_Mock
GSM4745315 g399_Mock
Relations
SRA SRP217465

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
GSE156844_RAW.tar 64.2 Mb (http)(custom) TAR (of TXT)
GSE156844_Raw_gene_counts_matrix_2.txt.gz 981.4 Kb (ftp)(http) TXT
GSE156844_gene_counts_TPM_matrix_2.txt.gz 2.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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