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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Katze

PROVIDER: E-GEOD-56678 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates.

Selinger Christian C Tisoncik-Go Jennifer J Menachery Vineet D VD Agnihothram Sudhakar S Law G Lynn GL Chang Jean J Kelly Sara M SM Sova Pavel P Baric Ralph S RS Katze Michael G MG

BMC genomics 20141222

<h4>Background</h4>The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic and pathogenic potential of emerging coronaviruses in humans. Clinical features of Middle East respiratory syndrome (MERS) include atypical pneumonia and progressive respiratory failure that is highly reminiscent of severe acute respiratory syndrome (SARS) caused by SARS-CoV. The host response is a key component of highly pathogenic respiratory virus infection. He ...[more]

PMID: 25534508

Similar Datasets

Cell host-response to infection with novel human coronavirus EMC predict potential antivirals and important differences with SARS-coronavirus.

Project description:Differential expression was determined in Calu-3 cells between mock infected and infection with either Human coronavirus EMC and SARS coronavirus at different times post infection. Calu-3 2B4 cells were infected with Human Coronavirus EMC 2012 (HCoV-EMC) or mock infected. Samples were collected 0, 3, 7, 12, 18 and 24 hpi. There are 3 mock and 3 infected replicates for each time point, except for 12 hpi for which there are only 2 infected replicates (one replicate did not pass RNA quality check). There were no mock sampes at 18 hpi, and therefore infected samples at 18 hpi were compared with mocks at 24 hpi. For direct comparison with SARS-CoV infected cells, raw data from HCoV-EMC experiments were quantile normalized together with the SARS-CoV dataset (GEO Series accession number GSE33267).

2013-05-03 | E-GEOD-45042 | 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. 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

Cytokine stimulation systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates.

Project description:Background: The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic potential of coronaviruses and the severe disease these etiologic agents can cause in humans. Clinical features of Middle East respiratory syndrome (MERS) include severe acute pneumonia and renal failure that is highly reminiscent of severe acute respiratory syndrome (SARS) caused by SARS-CoV. The host response is a key component of highly pathogenic respiratory virus infection. Here, we computationally analyzed gene expression changes in a human airway epithelial cell line infected with two genetically distinct MERS-CoV strains obtained from human patients, MERS-CoV-EMC (designated EMC) and MERS-CoV-London (designated LoCoV). Results: Using topological techniques, such as persistence homology and filtered clustering, we characterized the host response system to the different MERS-CoVs, with LoCoV inducing early kinetic changes, between 3 and 12 hours post infection, compared to EMC. Robust transcriptional changes distinguished the two MERS-CoV strains predominantly at the late time points. Combining statistical analysis of infection and cytokine-stimulated treatment transcriptomics, we identified differential innate and pro-inflammatory responses between the two virus strains, including up-regulation of extracellular remodeling genes following LoCoV infection and differential pro-inflammatory responses between the two strains. Conclusions: These transcriptional differences may be the result of amino acid differences in viral proteins known to modulate innate immunity against MERS infection. Triplicate wells of Calu-3 2B4 cells were infected with Human Coronavirus EMC 2012 (HCoV-EMC) or time-matched mock infected. Cells were harvested at 0, 3, 7, 12, 18 and 24 hours post-infection (hpi), RNA extracted and transcriptomics analyzed by microarray.

2014-08-31 | E-GEOD-56677 | biostudies-arrayexpress

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

TCL001: Calu-3 cells treated with either IFN alpha or gamma

Project description:Purpose of experiment was to compare transcriptomics of Calu-3 cells treated with either INF alpha or gamma. Calu-3 cells were treated with 1000 Units/ml of INFa (Sigma I4276) or 500 Units/ml of IFN γ (Sigma I3265). Cells were collected for RNA isolation at 0, 3, 6, and 18 or 22 h post treatment. Each treated 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. The NIAID Systems Virology Center

2011-11-01 | E-GEOD-33264 | biostudies-arrayexpress

ICL0012 - Host response in human Calu-3 cells to infection with NS1trunc124: A/Vietnam/1203-CIP048_RG4/2004 (H5N1) or WT: A/Vietnam/1203/2004 (H5N1)

Project description:Differential expression was determined in Calu-3 cells between mock infected and infection with NS1trunc124: A/Vietnam/1203-CIP048_RG4/2004 (H5N1) or WT: A/Vietnam/1203/2004 (H5N1) at different times post infection. Purpose: To obtain samples for transcriptional analysis in triplicate using the VN1203 pathogenicity mutant NS1-trunc124. Overview of Experiment: . Time Points: 0, 3, 7, 12, 18 and 24 hrs post infection. . Done in triplicate. . Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates. . Time-matched mocks were done in triplicate from the same cell stock as the rest of the samples. . Culture medium (the same as what the virus stock is in) was used for the mock infections. Calu-3 cells were infected with NS1trunc124: A/Vietnam/1203-CIP048_RG4/2004 (H5N1) or mock infected and samples were collected at 0, 3, 7, 12, 18 and 24 hpi. Calu-3 cells were infected with WT: A/Vietnam/1203/2004 (H5N1) and samples were collected at 7 and 24 hpi. There are 3 mock (2 included here) and 3 infected replicates for each time point. Expression profiles were determined.

2013-01-05 | E-GEOD-43204 | biostudies-arrayexpress

ICL002: Time course of Calu-3 cells infected with Influenza A/VN/1203/04

Project description:Purpose of experiment was to perform transcriptomics on Calu- 3 cells infected with Influenza A/VN/1203/04. Calu-3 cells were infected with Influenza A/VN/1203/04, at MOI of 1.0. Cells samples were collected at 0, 3, 7, 12, 18, and 24 h post infection. Each infected sample was done in duplicate. (Duplicates are defined as 2 different wells, plated at the same time using the same cell stock for all replicates.)There is one 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-33142 | biostudies-arrayexpress

ICL0011 - Host response in human Calu-3 cells to infection with A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB1-F2 deletion), A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB2-627E mutant) or WT: A/Vietnam/1203/2004 (H5N1)

Project description:Differential expression was determined in Calu-3 cells between mock infected and infection with one of 3 Influenza viruses (wild-type VN1203, VN1203 mutant PB1-F2del, VN1203 mutant PB2-627E) at different times post infection. Purpose: To obtain samples for transcriptional analysis in triplicate using the VN1203 pathogenicity mutants PB1-F2del and PB2-627E. Overview of Experiment: . Time Points: 0, 3, 7, 12, 18 and 24 hrs post infection. . There are two time points for wild type VN1203. . Done in triplicate. . Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates. . Time-matched mocks were done in triplicate from the same cell stock as the rest of the samples. . Culture medium (the same as what the virus stock is in) was used for the mock infections. Calu-3 cells were infected with A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB1-F2 deletion), A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB2-627E mutant) or mock infected and samples were collected at 0, 3, 7, 12, 18 and 24 hpi. Calu-3 cells were infected with WT: A/Vietnam/1203/2004 (H5N1) and samples were collected at 7 and 24 hpi. There are 3 mock and 3 infected replicates for each time point. Expression profiles were determined.

2013-01-05 | E-GEOD-43203 | 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.

2014-08-31 | GSE56678 | GEO

Host Regulatory Network Response in Calu-3 cell Infection with A/CA/04/2009 Influenza virus

Project description:Differential Expression was determined in Calu-3 cells between mock infected and infection with A/CA/04/2009 Influenza virus at nime time points post infection. Calu-3 cells were infected with A/CA/04/2009 Influenza virus at MOI of 3, samples were collected 0,3,7,12,18, 24, 30, 36 and 48 hpi. Expression profiles and DE genes were determined for all time points. There are 3 mock and infected replicates for each time point.

2012-05-04 | E-GEOD-37571 | biostudies-arrayexpress

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