Demethylation profiling of human lung cancer cell lines
Ontology highlight
ABSTRACT: 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).
Project description:Polycomb-mediated repression of Dkk-1 activates Wnt signaling and enhances tumorigenic potential of lung cancer cells following tobacco smoke exposure Experiment Overall Design: microarray techniques were used to examine proliferation and gene expression in A549 and Calu-6 lung cancer cells cultured in normal media with or without tobacco smoke condensate (TSC)
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.
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.
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.
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.
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.
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.
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
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.
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