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)
Project description:The purpose of this experiment was to obtain samples for transcriptome analysis using wild-type viruses: Zaire Ebola (ZEBOV '76) and Reston Ebola (REBOV '08). Overview of Experiment: Cells: Immortalized Human Hepatocytes (IHH); seed 60,000 cells per well in a 24-well plate. Infected with a multiplicity of infection (MOI) of 0.5. After infection, 3x wash with PBS and replace with 5% FCS DMEM without NaPyr or NEAA. Time matched mocks done in triplicate from same cell stock as rest of samples. Time Points = 0, 8, 24, 48, and 72 hrs post infection in triplicate. (For miRNA: 8, 24, 48, 72 hours.)
Project description:The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with WT A/Anhui/1/2013 (H7N9; 'AH1'), and AH - NS1-103F/106M. Human Calu-3 cells were seeded at 1 x 10^6 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 1. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 7 and 12 h post-infection
Project description:The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with WT A/Anhui/1/2013 (H7N9; 'AH1'), AH - NS1-103F/106M, and AH1 - 691 (ferret adapted virus). Human Calu-3 cells were seeded at 1 x 10^6 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 1. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 7, 12 and 24 h post-infection
Project description:The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with wild-type A/Vietnam/1203/2004 (H5N1; 'VN1203'; derived by reverse genetics), PB2-K627E (627K is a mammalian-adapting mutation that increases polymerase replicatve activity; '627E' is typically found in avian species), and NS1-trunc124 (this 'NS1' protein has a 90 amino acid truncation at the C-terminus). Human Calu-3 cells were seeded at 1 x 10^6 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 1. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 7, 12, and 24 hr post-infection.
Project description:The purpose is to obtain samples for mRNA and miRNA analysis with and without interferon α treatment; in parallel, to obtain cell pellets to forward to PNNL for use in top-down proteomics pilot experiments Human Calu-3 cells were seeded at 1 x 10^6 cells per well on 6 well plates 3 days before infection. Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 500 U/ml of human interferon α (PBL Biosciences). Mock-treated cells were given normal culture medium only. Mock and treated cells were incubated at 37°C until sample collection time points. Infected samples were collected in quadruplet; time-matched mocks were collected in quadruplet in parallel with infected samples. Time points: 6, 12, and 18 h post-infection
Project description:The purpose is to obtain samples for mRNA and miRNA analysis with and without interferon α treatment; in parallel, to obtain cell pellets to forward to PNNL for use in top-down proteomics pilot experiments Human Calu-3 cells were seeded at 1 x 10^6 cells per well on 6 well plates 3 days before infection. Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 500 U/ml of human interferon α (PBL Biosciences). Mock-treated cells were given normal culture medium only. Mock and treated cells were incubated at 37°C until sample collection time points. Infected samples were collected in quadruplet; time-matched mocks were collected in quadruplet in parallel with infected samples. Time points: 6, 12, and 18 h post-infection
Project description:The purpose is to obtain samples for transcriptional analysis in triplicate wells using wild type West Nile virus (WNV NY99 clone 382; WNVWT) and mutant virus (WNVE218A) in mouse granule cell neurons. This data set comprises two complete biological replicate experiments conducted in the same conditions and with data processed independently. Granule cell neurons from day 6 C57Bl/6J mouse pups are infected with plasmid-derived wild type West Nile virus NY99 clone 382 (WNVWT) or plasmid-derived isogenic E218A mutant West Nile virus NY99 clone 382 (WNVE218A) with multiplicity of infection (MOI) 250. Three technical replicates were performed at each of 1, 8, 12 and 24 hrs post infection. Time matched mocks done in triplicate are treated with mockulum: cell media concentrated through ultracentrifugation and diluted as virus. mRNA is sampled at all time points; microRNA is sampled at 12 hours post-infection. There were two independent biological replicates of the entire procedure, distinguished by sample name prefixes ('WGCN002' and 'WGCN003') and the biological_replicate characteristic field.
Project description:The purpose is to obtain samples for transcriptional analysis in triplicate wells using wild type West Nile virus (WNV NY99 clone 382; WNVWT) and mutant virus (WNVE218A) in mouse cortical neurons. This data set comprises two complete biological replicate experiments conducted in the same conditions and with data processed independently. Primary cortical neurons from C57Bl/6J mouse embryos (age E15) are infected with plasmid-derived wild type West Nile virus NY99 clone 382 (WNVWT) or plasmid-derived isogenic E218A mutant West Nile virus NY99 clone 382 (WNVE218A) with multiplicity of infection (MOI) 250. Three technical replicates were performed at each of 1, 8, 12 and 24 hrs post infection. Time matched mocks done in triplicate are treated with mockulum: cell media concentrated through ultracentrifugation and diluted as virus. mRNA is sampled at all time points; microRNA is sampled at 12 hours post-infection. There were two independent biological replicates of the entire procedure, distinguished by sample name prefixes ('WCN002' and 'WCN003') and the biological_replicate characteristic field.
Project description:The study profiles genome-wide mRNA expression in blood from 18 early-onset SZ (EOS) cases and 12 healthy controls. A total of 1070 mRNAs were detected by the microarrays in our samples. 18 schizophrenia samples and 12 healthy controls were used to acquire blood expression profiles