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Series GSE191315 Query DataSets for GSE191315
Status Public on Apr 26, 2023
Title In vivo single-cell profiling of lncRNAs during Ebola virus infection (SABio)
Organism Macaca mulatta
Experiment type Expression profiling by high throughput sequencing
Summary Long non-coding RNAs (lncRNAs) are pivotal mediators of systemic immune response to viral infection yet most studies concerning their expression and functions upon immune stimulation are limited to in vitro bulk cell populations. This strongly constrains our understanding of how lncRNA expression varies at single-cell resolution, and whether differences with protein coding genes exist in their cell-type specific immune regulatory roles. Here, we perform the first in-depth characterization of lncRNA expression variation at single-cell resolution during Ebola virus (EBOV) infection in vivo. Using bulk RNA-sequencing from 119 samples and 12 tissue types, we significantly expand the current macaque lncRNA annotation. We then profile lncRNA expression variation in immune circulating single-cells during EBOV infection and find that lncRNAs’ expression in fewer cells is a major differentiating factor to their protein coding gene counterparts. Upon EBOV infection, lncRNAs present dynamic and mostly cell-type specific changes in their expression profiles especially in monocytes, the main cell type targeted by EBOV. Such changes are associated with gene regulatory modules related to important innate immune responses such as interferon response and purine metabolism. Within infected cells, several lncRNAs have correlated and anti-correlated expression with viral load, suggesting that expression of some of these lncRNAs might be directly hijacked by EBOV to attack host cells. This study provides novel insights on the roles that lncRNAs play in the host response to acute viral infection and paves the way for future lncRNA studies at single-cell resolution.
 
Overall design Bulk RNA sequencing of tissues from infected macaques infected with EBOV. Some of the macaques were subministered an anti-Ebola virus IgG immunoglobulins cocktail.
 
Contributor(s) Santus L
Citation(s) 37391481
Submission date Dec 20, 2021
Last update date Jul 26, 2023
Contact name luisa santus
E-mail(s) luisa.santus95@gmail.com
Phone +34667249041
Organization name Barcelona Supercomputing Center
Street address Plaça d'Eusebi Güell, 1-3
City Barcelona
ZIP/Postal code 08034
Country Spain
 
Platforms (1)
GPL19129 Illumina HiSeq 2500 (Macaca mulatta)
Samples (57)
GSM5743442 SABio_Adrenal_CtrlAb_NHP6
GSM5743443 SABio_Adrenal_EbovAb_NHP10
GSM5743444 SABio_Adrenal_EbovAb_NHP11
This SubSeries is part of SuperSeries:
GSE192447 In vivo single-cell profiling of lncRNAs during Ebola virus infection.
Relations
BioProject PRJNA790971

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

Supplementary file Size Download File type/resource
GSE191315_RAW.tar 241.4 Mb (http)(custom) TAR (of GTF)
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Raw data are available in SRA
Processed data provided as supplementary file

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