Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of SARS-CoV-2 infection on gene expression of iPSC derived sensory neurons [bulkRNAseq]

ABSTRACT: To investigate the impact of SARS-CoV-2 on the peripheral nervous system, we generated human sensory neurons from induced pluripotent stem cells (iPSC) that we further infected with the SARS-CoV-2 strain WA1/2020 for 48 hours. We then performed gene expression profiling analysis using data obtained from RNA-seq of mock treated cells compared to SARS-CoV-2 infected cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE227528 | GEO | 2023/08/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of SARS-CoV-2 infection on gene expression of iPSC derived sensory neurons [scRNAseq]

Project description:To investigate the impact of SARS-CoV-2 on the peripheral nervous system, we generated human sensory neurons from induced pluripotent stem cells (iPSC) that we further infected with the SARS-CoV-2 strain WA1/2020 for 48 hours.

2023-08-04 | GSE227529 | GEO

Gene expression of SARS-CoV-2-infected Vero E6 cells

Project description:We conducted a high-throughput drug repositioning screen using the LOPAC®1280 and the ReFRAME drug libraries to identify existing drugs that harbor antiviral activity against SARS-CoV-2, in a Vero E6 cell-based assay. We additionally performed RNA sequencing on control and SARS-CoV-2 infected Vero E6 cells to study the biological changes after SARS-CoV-2 infection and to elucidate the potential mechanisms underlying the positive hits identified from our high-throughput screen. Vero E6 cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI = 0.3) with three replicates. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

2020-07-08 | GSE153940 | GEO

A Single Intranasal Vaccination with a Rationally Attenuated SARS-CoV-2 Elicits Strong Humoral Immune Response and Is Protective in Syrian Hamsters

Project description:Very few live attenuated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are currently in pre-clinical or clinical development. We rationally attenuated SARS-CoV-2 (isolate WA1/2020) by removing the polybasic cleavage site within the spike protein and the open reading frames (ORFs) 6-8, and by introducing a pair of mutations into the non-structural protein 1 (Nsp1). The derived virus (WA1-DPRRA-ORF6-8-Nsp1K164A/H165A) became severely attenuated in both the K18-human ACE2 (hACE2) transgenic mice and in Syrian hamsters. Transcriptomic profiling of nasal turbinates and lung tissues of infected Syrian hamsters confirmed that WA1-DPRRA-ORF6-8-Nsp1K164A/H165A attenuated the upregulation of proinflammatory pathways. A single intranasal immunization of just 100 PFU of the WA1-DPRRA-ORF6-8-Nsp1K164A/H165A elicited binding and neutralizing antibody responses in Syrian hamsters and completely protected against SARS-CoV-2-induced weight loss and pneumonia. These data demonstrate the feasibility of rational attenuation of SARS-CoV-2. WA1-DPRRA-ORF6-8-Nsp1K164A/H165A represents a promising live attenuated vaccine candidate.

2022-04-04 | GSE199922 | GEO

Gene expression of SARS-CoV-2-infected Vero E6 cells with remdesivir treatment

Project description:RNA sequencing was performed on control and SARS-CoV-2 infected Vero E6 cells, with or without remdesivir treatment to study the biological changes after SARS-CoV-2 infection and to evaluate the effectiveness of remdesivir on the gene expression level. 500,000 Vero E6 cells were seeded in 6-well plates. The following day, the cell medium was replaced with fresh medium supplemented with either DMSO or 1 µM remdesivir, and cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI=0.3), with three replicates per experimental condition. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

2021-02-02 | GSE165955 | GEO

Viral and Host Small RNA Response to SARS-CoV-2 Infection

Project description:HEK293T cells overexpressing hACE2 were infected by SARS-CoV-2 (WA1) and small RNA-seq was performed to profile small RNAs in response to SARS-COV-2 infection

2022-10-08 | GSE189920 | GEO

The use of human iPSC-derived alveolar organoids to explore SARS-CoV-2 variant infections and host responses

Project description:The apical-in, sheared, and apical-out airway organoids (AOs) were infected with the SARS-CoV-2 WA1 isolate at a multiplicity of infection (MOI) of 0.25 for 72 hours. Subsequently, the total RNA was utilized for next-generation RNA sequencing in order to analyze and characterize the mRNA expression patterns.

2023-07-14 | GSE237059 | GEO

SARS-CoV-2 infection evokes transcriptional changes in Calu-3 cells and cultured primary mouse trigeminal ganglia cells

Project description:SARS-CoV-2, the virus responsible for COVID-19, infects both human airway epithelial cells and trigeminal ganglia. We assessed the consequences of SARS-CoV-2 infection on gene expression in Calu-3 cells and in primary Mus musculus trigeminal ganglia cells (mmTG). Here, we provide datasets that include raw reads and mapped reads for the following: 1) mock infected mmTG 48 hrs post infection; 2) SARS-CoV-2 infected mmTG 48 hrs post infection; 3) mock infected Calu-3 cells 24 hrs post infection; 4) SARS-CoV-2 infected Calu-3 cells 24 hrs post infection; 5) mock infected Calu-3 cells 48 hrs post infection; 6) SARS-CoV-2 infected Calu-3 cells 48 hrs post infection.

2024-01-08 | GSE252056 | GEO

Absence of host innate immune responses in SARS-CoV-infected ferrets upon subsequent challenge

Project description:To further investigate the underlying mechanisms of severe acute respiratory syndrome (SARS) pathogenesis and evaluate the therapeutic efficacy of potential drugs and vaccines it is necessary to use an animal model that is highly representative of the human condition in terms of respiratory anatomy, physiology and clinical sequelae. The ferret, Mustela putorius furo, supports SARS-CoV replication and displays many of the symptoms and pathological features seen in SARS-CoV-infected humans. We have recently established a SARS-CoV infection-challenge ferret platform for use in evaluating potential therapeutics to treat SARS. The main objective of the current study was to extend our previous results and identify early host immune responses upon infection and determine immune correlates of protection upon challenge with SARS-CoV in ferrets. Keywords: time course This study is a simple time course (58 day) examination of host responses in 35 SARS-CoV (TOR2) infected ferrets with the addition of a challenge inoculation of SARS CoV (TOR2) at day 29 post infection. Three mock-infected ferrets are included as negative controls. Due to the unavailability of ferret microarrays, Affymetrix Canine 2.0 oligonucleotide arrays were chosen following sequence analysis of our ferret cDNA library (~5000 clones) and demonstration of high levels of homology (>80%) between dog and ferret.

2013-05-28 | E-GEOD-11704 | biostudies-arrayexpress

Real-time quantitative PCR analysis of mouse lungs after exposure to SARS-CoV-2 and variants of concern (VOC)

Project description:Age-matched K18-hACE2 transgenic mice were infected intranasally with different SARS-CoV-2 viruses, including (1) USA-WA1/2020 (WA) of lineage A, (2) New York-PV09158/2020 (NY) of lineage B.1.3, (3) USA/CA_CDC_5574/2020 (CA) of lineage B.1.1.7 and (4) hCoV-19/South Africa/KRISP-EC-K005321/2020 (SA) of lineage B.1.351. Mouse lungs were harvested on 3 days post infection (dpi). Total RNA was extracted using QIAgen RNeasy Plus Mini Kit and was reverse transcribed using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Resultant cDNA was used as the template along with RT2 SYBR Green ROX qPCR Mastermix (Qiagen) to perform RT² Profiler™ PCR Array Mouse Hypoxia Signaling Pathway (Qiagen) real-time PCR in Stratagene MX3000p qPCR system.

2021-10-10 | GSE183621 | GEO

The PDZ-binding motif of SARS-CoV envelope protein is a determinant of viral pathogenesis

Project description:A recombinant SARS-CoV lacking the envelope (E) protein is attenuated in vivo. Here we report that E protein PDZ-binding motif (PBM), a domain involved in protein-protein interactions, is a major virulence determinant in vivo. Elimination of SARS-CoV E protein PBM by using reverse genetics led to attenuated viruses (SARS-CoV-mutPBM) and to a reduction in the deleterious exacerbate immune response triggered during infection with the parental virus (SARS-CoV-wt). Cellular protein syntenin bound E protein PBM during SARS-CoV infection. Syntenin activates p38 MAPK leading to overexpression of inflammatory cytokines, and we have shown that active p38 MAPK was reduced in lungs of mice infected with SARS-CoVs lacking E protein PBM (SARS-CoV-mutPBM) as compared with the parental virus (SARS-CoV-wt), leading to a decreased expression of inflammatory cytokines and to viral attenuation. Therefore, E protein PBM is a virulence factor that activates pathogenic immune response most likely by using syntenin as a mediator of p38 MAPK induced inflammation. Three biological replicates were independently hybridized (one channel per slide) for each sample type (SARS-CoV-wt, SARS-CoV-mutPBM, Mock). Slides were Sure Print G3 Agilent 8x60K Mouse (G4852A-028005)

2014-10-31 | E-GEOD-52920 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data