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SCL006,icSARS CoV Urbani or icSARS Bat SRBD (spike receptor binding domain from the wild type strain Urbani to allow for infection of human and non-human primate cells) infections of the 2B4 clonal derivative of Calu-3 cells - Time course

ABSTRACT: Purpose of experiment was to compare transcriptomics of 2B4 cells (clonal derivative of Calu-3 cells) infected with either icSARS CoV or the icSARS deltaORF6 mutant.

ORGANISM(S): Homo sapiens

PROVIDER: GSE37827 | GEO | 2012/05/07

SECONDARY ACCESSION(S): PRJNA163617

REPOSITORIES: GEO

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SCL006,icSARS CoV Urbani or icSARS Bat SRBD (spike receptor binding domain from the wild type strain Urbani to allow for infection of human and non-human primate cells) infections of the 2B4 clonal derivative of Calu-3 cells - Time course

Project description:Purpose of experiment was to compare transcriptomics of 2B4 cells (clonal derivative of Calu-3 cells) infected with either icSARS CoV or the icSARS deltaORF6 mutant. Calu-3 cells were infected with either icSARS CoV or the cSARS Bat SRBD strain at MOI of 1.0. Cells samples were collected at 0, 7, 12, 24, 30, 36, 48, 54, 60 or 72h post infection. Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the mock infections. Contributor: The NIAID Systems Virology Center

2012-05-06 | E-GEOD-37827 | biostudies-arrayexpress

SCL005: icSARS CoV Urbani or icSARS deltaORF6 infections of the 2B4 clonal derivative of Calu-3 cells - Time course

Project description:Purpose of experiment was to compare transcriptomics of 2B4 cells (clonal derivative of Calu-3 cells) infected with either icSARS CoV or the icSARS deltaORF6 mutant.

2011-11-01 | GSE33267 | GEO

SCL008: icSARS CoV, icSARS-deltaNSP16 or icSARS ExoNI infections of the 2B4 clonal derivative of Calu-3 cells - Time course

2014-05-23 | GSE48142 | GEO

SCL005: icSARS CoV Urbani or icSARS deltaORF6 infections of the 2B4 clonal derivative of Calu-3 cells - Time course

Project description:Purpose of experiment was to compare transcriptomics of 2B4 cells (clonal derivative of Calu-3 cells) infected with either icSARS CoV or the icSARS deltaORF6 mutant. Calu-3 cells were infected with either icSARS CoV or the icSARS deltaORF6 mutant at MOI of 5.0. Cells samples were collected at 0, 3, 7, 12, 24, 30, 36, 48, 54, 60 or 72h post infection. Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the mock infections. The NIAID Systems Virology Center

2011-11-01 | E-GEOD-33267 | biostudies-arrayexpress

SCL008: icSARS CoV, icSARS-deltaNSP16 or icSARS ExoNI infections of the 2B4 clonal derivative of Calu-3 cells - Time course

Project description:Purpose of experiment was to compare transcriptomics of 2B4 cells (clonal derivative of Calu-3 cells) infected with either icSARS CoV, icSARS-deltaNSP16 or icSARS ExoNI mutants. 2B-4 cells (clonal derivatives of Calu-3 cells) were infected with either icSARS CoV, icSARS deltaNSP16 or icSARS ExoNI. Wild type and deltaNSP16 mutant infections were at an MOI of 5 while the ExoNI infections were at an MOI of 1. Cells samples were collected at 0, 7, 12, 24, 36, 36, 48, 60 or 72h post infection. Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.) There are triplicate time-matched Mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the Mock infections.

2014-05-23 | E-GEOD-48142 | biostudies-arrayexpress

Transcriptional analysis of Calu-3 2B-4 cells stimulated with Interleukin-1a and TNFa.

Project description:Calu-3 2B-4 cells were stimulated with interleukin-1a or TNFa. Transcriptional analysis of the extracted RNA was done by microarray. Calu-3 2B-4 cells were washed with phosphate-buffered saline (PBS) and treated with either IL-1a (0.001ng/ml) or TNFa (0.05ng/ml) or mock diluted in PBS for 40 min at 37C. Following treatment, cells were washed 3 times, and fresh medium was added. Triplicate Calu-3 2B4 cultures and triplicate time-matched mock-infected controls were harvested at 3, 6 and 24h for IL-1a and 6 and 24h for TNF post-exposure for transcriptional analysis.

2014-08-31 | E-GEOD-56678 | biostudies-arrayexpress

Prochlorothrix hollandica PCC 9006 = CALU 1027 isolate:CALU 1027

Project description:Prochlorothrix hollandica PCC 9006 = CALU 1027 isolate:CALU 1027 Genome sequencing and assembly

| PRJNA63021 | ENA

Whole transcriptome exploration revealed the dysregulated RNAs involved in SARS-CoV-2 spike protein inhibited apoptosis in Calu-3 cells

Project description:SARS-CoV-2 induced COVID-19 has been spreading all over the world since 2020. Although the vaccines have been planted and efficiently suppressed the momentum, it is not fully understood how SARS-CoV-2 infects host cells, especially for the functions of its spike (S) glycoprotein. In this study, we investigated the biological and molecular functions of S protein by infecting the commercial pure S protein into human Calu-3 cells and analyzing apoptotic level change and its regulated transcriptome profile using whole transcriptome sequencing method (RNA-seq). Strikingly, we found S protein alone could significantly inhibit apoptotic level with dose dependent manner in Calu-3 cells, with or without ActD treatment. Higher level of S protein has more effective inhibition on cellular apoptosis. ActD-treated RNA-seq data analysis revealed hundreds of mRNAs, lncRNAs, and circRNAs were differentially expressed at post-transcriptional level. Functional enrichment analysis of DE mRNAs and lncRNAs showed they were highly enriched in inflammatory response, cell adhesion, and apoptotic process pathways. Host genes of circRNAs were enriched in metabolic and lysosome pathways. Finally, we constructed an RNA regulatory network involving these three RNA classes that were dysregulated in this study. RT-qPCR experiment was performed to validate the DE RNAs, which showed a high consistency with RNA-seq data. In conclusion, our study demonstrated the novel functions of SARS-CoV-2 S protein in lung Calu-3 cells, which will be helpful to understand the underlying molecular mechanisms during SARS-CoV-2 infection and the development of drugs and vaccines in future.

2025-04-22 | GSE201325 | GEO

Nostoc sp. CALU 546

Project description:Nostoc sp. CALU 546 Genome sequencing

| PRJNA1021510 | ENA

Human Calu-3 cell transcriptome response to a wild type infectious clone of Middle Eastern Respiratory Syndrome (icMERS) coronavirus and icMERS mutant viruses

Project description:The purpose of this experiment was to obtain samples for transcriptome analysis using wild type infectious clone of Middle Eastern Respiratory Syndrome (icMERS) coronavirus and icMERS mutant viruses: icMERS-RFP, icMERS-dNSP16, icMERS-d4B, and icMERS-d3-5. For protocol details, please search for the protocol ID at https://systemsvirology.org. Overview of Experiment: Cells: 2B4 Calu-3 cells; seed 5 x 10^5 cells per well on 6 well plates 2 days before infection. Prior to infection, washed cells 2 times with PBS, and then infected with a multiplicity of infection of 5. Time matched mocks done in triplicate from same cell stock as rest of samples using culture medium. Time points: 0, 7, 12 and 24 h post-infection (For miRNA: 7, 12 hours only)

2015-02-04 | E-GEOD-65574 | biostudies-arrayexpress

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