Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA-sequencing of A549 cells transduced with Ad5 empty vector (GFP) or Ad5 expressing SARS-CcV-2 nucleocapsid (AdN)

ABSTRACT: To investigate how the abundant expression of SARS-CoV-2 nucleocapsid might change the transcriptome, A549 human lung carcinoma cells were transduced with replication-deficient recombinant human adenovirus type‐5 expressing SARS-CcV-2 nucleocapsid (AdN) or the empty vetor (GFP). Twenty-four hours later, the transduced cells were subjected to bulk RNA sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE231733 | GEO | 2026/05/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Chromatin disruptions in pathophysiologically relevant gene promoters underlie unique SARS-Cov-2 nucleocapsid-mediated gene regulation

Project description:SARS-CoV-2, the causative agent of COVID-19, is a positive-sense, single-stranded RNA virus that causes a spectrum of disease severity, from asymptomatic infection to severe illness to long-term sequelae. Similar to other human coronaviruses, SARS-CoV-2 proteins modulate host genomic responses through epigenomic modifications, facilitating viral replication and immune evasion. While the nucleocapsid protein is well known for its role in RNA stability and immune modulation, its impact on host chromatin organization remains unclear. To investigate this, we generated stable human alveolar cell lines expressing nucleocapsid proteins from endemic and pandemic human coronaviruses. Our analysis revealed that nucleocapsid proteins from all tested coronaviruses induced changes in nucleosome positioning and occupancy at specific gene promoters involved in coagulation pathways, hormone signaling, and innate immune responses. Additionally, SARS-CoV-2-specific alterations were identified in genes dysregulated in severe infections, such as suggesting a direct role for epigenomic modifications in disease pathophysiology. We also observed extensive changes in nucleosome susceptibility to nuclease digestion in SARS-CoV and SARS-CoV-2 samples that were not observed in common cold cell lines. Promoters with altered sensitivity and resistance to nuclease were linked to innate immune, metabolic, olfactory, and signaling pathways known to be dysregulated in severe COVID-19 and post-acute sequelae (PASC). These findings demonstrate that nucleocapsid protein expression alters chromatin structure at specific loci, implicating viral proteins in host genome dysregulation. Furthermore, we identified both shared and unique chromatin targets of SARS-CoV-2 and common cold coronaviruses, highlighting pathways for further investigation and potential therapeutic intervention.

2025-02-26 | GSE290042 | GEO

RNA-Seq of SARS-CoV-2 Nucleocapsid protein expression in human embryonic kidney cell line HEK293

Project description:The RNA genome of the SARS-CoV-2 virus encodes for four structural proteins, 16 non-structural proteins and nine putative accessory factors. A high throughput analysis of interactions between human and SARS-CoV-2 proteins identified multiple interactions of the structural Nucleocapsid (N) protein with RNA processing factors. The N-protein, which is responsible for packaging of the viral genomic RNA was found to interact with two RNA helicases, UPF1 and MOV10 that are involved in nonsense-mediated mRNA decay (NMD). NMD is a translation-coupled mechanism that targets mRNAs harboring a premature stop codon (PTC) for degradation, thereby serving as a quality control and gene regulatory pathway ensuring transcriptome integrity. Here, we wanted to explore the impact of transiently expressed N protein on the transcriptome of human embryonic kidney cell line HEK293 by RNA-Sequencing. To this end, the SARS-CoV2-N protein was transiently expressed from a pcDNA3.1-HA-N plasmid for 48 hours and the corresponding empty vector was used as a control.

2024-09-16 | E-MTAB-14342 | biostudies-arrayexpress

Vector-transduced neurons transcriptome profiles

Project description:With the goal of specifically dissecting the toxicogenomic signatures of the helper-dependent (HD) human (HAd5) and canine (CAV-2) adenovirus, the VSV-G-pseudotyped SIN HIV-1 (LV) and the Adenoviral-associated vector 2/9 for human neurons (AAV2/9), we transduced a bona fide human neuronal system with HD-HAd5, HD-CAV-2, LV and AAV2/9, we analysed the transcriptional response of more than 47,000 transcripts using gene chips. Chip data showed that HD-CAV-2 and LV vectors both activated the innate arm of the immune response, including Toll-like receptors and hyaluronan circuits. LV vector induced as well an IFN response. Moreover, HD-CAV-2 and LV vectors affected DNA damage pathways - at 5 days in opposite directions - suggesting a differential response of the p53 and ATM pathways to the vector genomes. As a general response to the vectors, human neurons activated pro-survival genes and neuron morphogenesis.

2013-05-22 | GSE47130 | GEO

Transcription profiling of human mammary epithelial cells transduced with either hTERT, empty LXSN vector or empty BABE vector

Project description:Analysis of gene expression in mammary epithelial cells transduced with either hTERT, empty LXSN vector or empty BABE vector.

2007-12-13 | E-GEOD-361 | biostudies-arrayexpress

Transcription profiling of human colon cells transduced with vector expressing thymosin beta4 antisense RNA are compared with empty vector-transduced cells

Project description:cells transduced with vector expressing thymosin beta4 antisense RNA are compared with empty vector-transduced cells

2010-09-01 | E-MEXP-2563 | biostudies-arrayexpress

Vector-transduced neurons transcriptome profiles

2013-05-22 | E-GEOD-47130 | biostudies-arrayexpress

Expression data of PRDM1α or empty vector-transduced NK92 or KHYG1 cell lines

Project description:CD25 (IL2RA) is a subunit of IL2 receptor complex, which determines the sensitivity of the receptor to IL2. Here, we investigated whether PRDM1, a transcriptional repressor implicated as a tumor suppressor in NK cell malignancies, directly represses CD25 (IL2RA). Using ChIP-seq, we identified a direct binding site of PRDM1 within 1st intron of CD25 (IL2RA) in activated primary human NK cells. We used DNA microarrays on two PRDM1α transduced NK cell lines (i.e. NK92 and KHYG1) to address whether PRDM1 transcriptionally represses CD25.

2021-05-05 | GSE157206 | GEO

Gene expression of CTCL cell line MyLa transduced with Empty-GFP or miR-26a-GFP expressing vector

Project description:By using a CTCL cell line MyLa transduced Empty-GFP or miR-26a-GFP, we conducted whole genome gene screening against the cells.

2021-07-21 | GSE180472 | GEO

Genome wide RNA-sequencing of human pluripotent stem-cell derived endothelial cells 48h after transduction with adenoviruses expressing either empty vector of different combination of transcription factors

Project description:To induce barrier of stem-cell derived endothelial cells in vitro cells have been transduced with a mixture of adenovirus overexpressing transcription factors with potential role in endothelial cell barrier stabilization. Adenoviruses overexpressing ETS1, SOX18 and SOX7 have been part of both transcription factor mixtures. As fourth transcription factor in the mixture included TAL1 while the other mixture included LEF1. Each transcription factor was used at 20 MOI. As control adenovirus overexpressing empty vectors has been used (80 MOI).

2020-03-05 | GSE142131 | GEO

Neuro-PASC is characterized by enhanced CD4+ and diminished CD8+ T cell responses to SARS-CoV-2 Nucleocapsid protein

Project description:Many people experiencing long COVID symptoms, or post-acute sequelae of SARS-CoV-2 infection (PASC), suffer from debilitating neurologic symptoms (Neuro-PASC). Although symptoms of Neuro-PASC are widely documented, it is still unclear whether virus-specific adaptive immunity is affected in these individuals. We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated CD4+ T cell responses toward the C-terminal region of SARS-CoV-2 Nucleocapsid protein when examined both functionally and using TCR sequencing. In contrast, Neuro-PASC patients also have diminished activation of CD8+ memory T cells and increased IL-6 production to Nucleocapsid. Elevated plasma immunoregulatory and reduced pro-inflammatory and antiviral response signatures were evident in Neuro-PASC patients compared with COVID convalescent controls without lasting symptoms, correlating with worse neurocognitive dysfunction. These data provide new insight into the impact of virus-specific cellular immunity on the pathogenesis of long COVID and pave the way for the rational design of predictive biomarkers and therapeutic interventions.

2023-05-24 | GSE225942 | GEO

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