Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq of Calu-3 epithelial cells treated with Cyclosporin A

ABSTRACT: Calu-3 cells are human lung cancer cells that serve as a model of respiratory epithelial cell model. Here, Calu-3 cells are used as a cell system for Middle East respiratory syndrome coronavirus and treated with Cyclosporin A To assess the effect of Cyclosporin A on the host cells, uninfected cells were treated with CsA or DMSO, RNA was extracted and compared against the DMSO treated control cells.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Homo sapiens

SUBMITTER: Judith Hoppe

PROVIDER: E-MTAB-8222 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

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

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

ICL010 - Infection of Calu-3 cells with H1N1 influenza virus A/Netherlands/602/2009

Project description:Differential expression was determined in Calu-3 cells between mock infected and infected with H1N1 influenza virus A/Netherlands/602/2009 at nine time points post-infection. As a comparison, cells were also infected with A/CA/04/2009 H1N1 influenza virus at 4 time points post-infection. Cells were infected at an MOI of 3.0. For the A/Netherlands/602/09-infected and mock-infected cells, samples were collected at 0, 3, 7, 12, 18, 24, 30, 36, and 48 hours post-infection (h.p.i.). For the A/California/04/2009-infected cells, samples were collected at 0, 12, 24, and 48 h.p.i. Samples were collected in triplicate.

2012-09-13 | E-GEOD-40844 | biostudies-arrayexpress

Demethylation profiling of human lung cancer cell lines

Project description:The goal of this study is to identify those genes that are commonly silenced by DNA-methylation in lung cancer cell lines. Experiment Overall Design: Ten lung cancer cell lines (Calu 1, Hotz, U1752, Calu 6, ZL25, Calu3, SW2, A549, H125, and H 460) were analyzed before and after the treatment with 5-aza-2âdeoxycitidine and trychostatin A (5AzaC/TSA).

2009-08-09 | E-GEOD-14315 | biostudies-arrayexpress

Transcriptomics analysis of SARS-CoV2-induced changes in human lung epithelial Calu-3 cells

Project description:RNA-Seq was carried out in order to obtain the time dependent expression dynamics of SARS-CoV2 (Trondheim strain)-induced transcriptome changes in human lung epithelial Calu-3 cells.

2022-10-25 | E-MTAB-12134 | 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

Allicin inhibits SARS-CoV-2 replication and abrogates the antiviral host response in the Calu-3 proteome

Project description:The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic causes a major health burden. Garlic organosulfur compounds, such as the diallyl thiosulfinate allicin exert strong antimicrobial activity against various respiratory pathogens. Here, we investigated the antiviral activity of allicin against SARS-CoV-2 in infected Vero E6 and Calu-3 lung cells. Allicin efficiently inhibited viral replication and infectivity in both cell lines. Proteome analyses of infected Calu-3 cells revealed a strong induction of the antiviral interferon-stimulated gene (ISG) signature (e.g. Mx1, IFIT, 2’5’OAS and ISG15), pathways of vesicular transport, tight junctions (KIF5A/B/C, OSBPL2, CLTC1, ARHGAP17) and ubiquitin modification (UBE2L3/5), as well as reprogramming of host metabolism, transcription and translation. Allicin abrogated the ISG host response and reverted the host cellular pathways to Mock levels, confirming the antiviral and immunomodulatory activity of allicin in the host proteome. Thus, biocompatible doses of garlic could be promising for protection of lung cells against SARS-CoV-2.

2021-06-30 | PXD024375 | Pride

Dazl is required for TET-mediated reprogramming to a naïve pluripotent state

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-07-01 | E-GEOD-69357 | biostudies-arrayexpress