Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes

ABSTRACT: In order to better understand the biological roles of critical SARS-CoV-2 proteins, we determined and compared the host transcriptomic responses of the HL-CZ human promonocytic cell line upon transfection with key viral genes encoding the spike S1 subunit, S2 subunit, nucleocapsid (NP) protein, NSP15 (endoribonuclease), and NSP16 (2′-O-ribose-methyltransferase).

ORGANISM(S): Homo sapiens

PROVIDER: GSE171080 | GEO | 2021/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes.

Project description: Not available

| S-EPMC8228226 | biostudies-literature

Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes

Project description:Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes

| PRJNA718288 | ENA

Spike Glycoprotein S1 Site-specific O-glycosylation: Systematic and Comparative Analysis from Eleven Variants of SARS CoV-2

Project description:In this study, we provide a comprehensive characterization of O-glycosylation in eleven variants of SARS-CoV-2 S1 subunit recombinantly expressed in HEK293 cells.

2024-01-26 | PXD041282 | Pride

Spike S1 domain interactome in non-pulmonary systems: a role beyond the receptor recognition

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which, since 2019 in China, has rapidly become a worldwide pandemic. The aggressiveness and global spread were enhanced by the many SARS-CoV-2 variants that have been isolated up to now. These mutations affect mostly the viral glycoprotein Spike (S), the capsid protein mainly involved in the early stages of viral entry processes, through the recognition of specific receptors on the host cell surface. In particular, the subunit S1 of the Spike glycoprotein contains the Receptor Binding Domain (RBD) and it is responsible for the interaction with the angiotensin-converting enzyme 2 (ACE2). Although ACE2 is the primary Spike host receptor currently studied, it has been demonstrated that SARS-CoV-2 is also able to infect cells expressing low levels of ACE2, indicating that the virus may have alternative receptors on the host cells. The identification of the alternative receptors can better elucidate the pathogenicity and the tropism of SARS-CoV-2. Therefore, we investigated the Spike S1 interactomes, starting from host membrane proteins of non-pulmonary cell lines, such as human kidney (HK-2), normal colon (NCM460D), and colorectal adenocarcinoma (Caco-2). We employed an affinity purification-mass spectrometry (AP-MS) to pull down, from the membrane protein extracts of all cell lines, the protein partners of the recombinant form of the Spike S1 domain. The purified interactors were identified by a shotgun proteomics approach. The lists of S1 potential interacting proteins were then clusterized according to cellular localization, biological processes, and pathways, highlighting new possible S1 intracellular functions, crucial not only for the entrance mechanisms but also for viral replication and propagation processes.

2023-03-11 | PXD035709 | Pride

Project description:S1 Metagenome

| PRJNA550282 | ENA

Project description:S1 Metagenome

| PRJNA534029 | ENA

Rubrivivax gelatinosus S1 strain:S1

Project description:Rubrivivax gelatinosus S1 strain:S1 Genome sequencing

| PRJEA81949 | ENA

Melissococcus plutonius S1 strain:S1

Project description:Melissococcus plutonius S1 strain:S1 Genome sequencing

| PRJNA215018 | ENA

Staphylococcus aureus S1 strain:S1

Project description:Staphylococcus aureus S1 strain:S1 Genome sequencing and assembly

| PRJNA207810 | ENA

Anatomy of footprint extension in ribosome profiling reveals translational landscape mediated by S1 protein in bacteria

Project description:Ribosome profiling — RNase footprinting of ribosome-bound mRNA — has been a unique and powerful method, applied to widespread organisms to survey ribosome traversal along mRNAs. In contrast to eukaryotes, bacterial ribosome footprints show a broad range of sizes, reflecting the differential states of ribosomes. However, the origin remains unclear. Here, we show that rotated state of ribosomes and intramolecular RNA duplexes each extend bacterial ribosome footprints at the 5′ end. Combining elongation inhibitors, cryo-electron microscopy, and ribosome profiling, we demonstrated that the rotated state of ribosomes results in long footprints. Along the subunit rotation, ribosomal protein S1 — a 30S-subunit RNA-binding protein — sterically protects mRNA at the 5′ end of the ribosome from RNase digestion and facilitates elongation of the ribosome. Moreover, we found that ribosomes stalled on ycbZ mRNA generate prolonged footprints because of their unique RNA secondary structure proximal to ribosomes. Through the studies of footprint extension, our results revealed S1-mediated stabilization of translation elongation and provide ribosome profiling approach to probe the conformational diversity of ribosomes in bacteria.

2023-07-28 | GSE155243 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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