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Series GSE191317 Query DataSets for GSE191317
Status Public on Dec 01, 2023
Title Type-I interferome in human peripheral blood mononuclear cells (PBMC)
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: Commercially purchased PBMCs from 7 donors were mock treated or with ISRE activity normalized IFNa1, IFNa2, IFNa4, 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 (FWD) Prep Kit. RNASeq were performed on Illumina NovaSEQ6000.
Results: An average of 12.6 million gene counts were identified for each donor/treatment. A total of 50,133 genes were mapped, and among them 333 genes were differentially expressed due to type I interferon treatments. Each of IFNa subtypes or IFNb has their specifically regulated genes in PBMCs.
Conclusion: These are the further evidences that there are qualitative differences between type I interferons.
Overall design Transcriptomic profiles of PBMCs treated with different Type I interferons.
Contributor(s) Guo K, Barrett BS, Cooper E, Santiago ML
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BioProject PRJNA789251
Submission date Dec 20, 2021
Last update date Dec 01, 2023
Contact name Kejun Guo
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)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (56)
GSM5743508 D3Mock
GSM5743509 D3IFNa1
GSM5743510 D3IFNa2
SRA SRP350916

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
GSE191317_RAW.tar 19.5 Mb (http)(custom) TAR (of TXT)
GSE191317_Raw_gene_counts_matrix.txt.gz 2.6 Mb (ftp)(http) TXT
GSE191317_gene_counts_TPM_matrix.txt.gz 13.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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