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Project created: 27th Sep 2023
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- People (7)
- Institutions (1)
- Investigations (1)
- Studies (1)
- Assays (18+1)
- Data files (27)
- SOPs (13)
- Publications (1)
Projects: Zika Virus Investigation, STING - Adjuvant, IMPAc-TB Project
Institutions: University of Washington
https://orcid.org/0009-0003-6381-9603Expertise: Bioinformatics
Tools: R, Single Cell analysis, Genomics, Transcriptomics, Python
Projects: Zika Virus Investigation
Institutions: University of Washington
Projects: Zika Virus Investigation
Institutions: University of Washington
https://orcid.org/0000-0003-1381-265XProjects: Zika Virus Investigation
Institutions: University of Washington
Projects: Zika Virus Investigation
Institutions: University of Washington
Submitter: John Cornelius
Studies: Viral Protein Accumulation of Zika Virus Variants Links with Regulation ...
Assays: Bioinformatics analyses of NanoString data, Deep sequencing of ZIKV stocks and sequence alignment, FFU assay for determining the titers of ZIKV stocks, FFU assay for measuring viral spread, Flow cytometry, Immunoblot analysis, Immunofluorescence analysis, Plaque assay, Protein lysate quantification, Quantification of extracellular and intracellular RNA, Quantification of extracellular and intracellular virions, Sample - Metadata, Transcript analysis by NanoString, Transcript analysis by SYBR green qRT-PCR, Viral copy number quantification by TaqMan qRT-PCR, ZIKV attachment and entry assay, ZIKV infection, ZV-13 antibody purification and quantification
Snapshots: No snapshots
Asian lineage Zika virus (ZIKV) strains emerged globally, causing outbreaks linked with critical clinical disease outcomes unless the virus is effectively restricted by host immunity. We have previously shown that retinoic acid-inducible gene-I (RIG-I) senses ZIKV to trigger innate immunity to direct interferon (IFN) production and antiviral responses that can control ZIKV infection. However, ZIKV proteins have been demonstrated to antagonize IFN. Here, we conducted in vitro analyses to assess ...
Submitter: John Cornelius
Investigation: Zika Virus
Assays: Bioinformatics analyses of NanoString data, Deep sequencing of ZIKV stocks and sequence alignment, FFU assay for determining the titers of ZIKV stocks, FFU assay for measuring viral spread, Flow cytometry, Immunoblot analysis, Immunofluorescence analysis, Plaque assay, Protein lysate quantification, Quantification of extracellular and intracellular RNA, Quantification of extracellular and intracellular virions, Sample - Metadata, Transcript analysis by NanoString, Transcript analysis by SYBR green qRT-PCR, Viral copy number quantification by TaqMan qRT-PCR, ZIKV attachment and entry assay, ZIKV infection, ZV-13 antibody purification and quantification
Snapshots: No snapshots
ZIKV RNA was extracted from virus working stocks using the QIAmp viral RNA minikit (Qiagen, Hilden, Germany). Isolated RNA was then digested with DNase I and purified using the Qiagen RNeasy kit. RNA quality was analyzed on the 2100 bioanalyzer (Agilent, Santa Clara, CA, USA) using the Agilent RNA 6000 Pico assay and quantified on a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA) prior to rRNA depletion and RNA library prep using the KAPA HyperPrep kit (Roche Diagnostics Corporation, Indianapolis, ...
Submitter: John Cornelius
Assay type: RNA Sequencing
Technology type: Rna-seq
Investigation: Zika Virus
Hybridoma supernatant was harvested as the source of ZV-13 antibody once ~95% cell death was observed. The supernatant was clarified by centrifuging for 10 min at 400 × g at 4°C and then filtered with a 0.22-μm filter prior to antibody purification via protein A affinity chromatography using the Pierce Protein A IgG purification kit and NAb Protein A Plus spin columns (all from Thermo Fisher-Life Technologies). Purified ZV-13 antibody was concentrated and buffer-exchanged into 1× phosphate-buffered ...
Submitter: John Cornelius
Assay type: Immunoassay
Technology type: Affinity Chromatography
Investigation: Zika Virus
Organisms: No organisms
SOPs: Protein A ELISA Protocol 10-29-20, Protein A Purification
Data files: No Data files
Snapshots: No snapshots
A549 cells were seeded in 96-well plates at a density of 2 × 104 cells per well. The following day, virus stocks were serially diluted in DMEM containing 2% FBS (2% DMEM), and cells were inoculated with dilutions in triplicate at 37°C for 2 h. After the incubation, cells were overlaid with DMEM supplemented with 1% carboxymethylcellulose (Fisher Scientific), 2% FBS, 10 mM HEPES, and 1× penicillin/streptomycin. At 48 hpi, the methylcellulose overlay and medium were removed, and cells were fixed ...
Submitter: John Cornelius
Assay type: Organism or Strain Characteristics
Technology type: Immunostaining
Investigation: Zika Virus
Organisms: No organisms
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
A549 cells were seeded in 6-well plates at a density of 6 × 105 cells per well. The following day, virus stocks were serially diluted in 2% DMEM, and cells were inoculated and fixed as described above. Following fixation, cells were washed with 1× PBS, and an anti-flavivirus envelope antibody, 4G2 (Ab00230-2.0; Absolute Antibody, Oxford, UK), diluted 1:500 in permeabilization/wash/block buffer (see recipe above) was added to the cells. Following incubation with primary antibody, donkey anti-mouse ...
Submitter: John Cornelius
Assay type: Immunoassay
Technology type: Imaging
Investigation: Zika Virus
Organisms: No organisms
SOPs: AL_ZIKV FFU Assay Protocol_6 well plate
Data files: No Data files
Snapshots: No snapshots
A549 cells were seeded at a density of 3 × 105 cells per well in 12-well plates. Cells were uninfected, mock-infected, or infected with ZIKV variants the next day at an MOI of 5 FFU/cell, and virus inocula prepared in DMEM were allowed to adsorb at 37°C for 2 h with rocking. Uninfected samples are seeded cells that remained untouched throughout the infection time course, whereas mock-infected samples were inoculated with DMEM. Following adsorption, the inocula were removed, and cells were washed ...
Submitter: John Cornelius
Assay type: Cultivation Experiment
Technology type: Technology Type
Investigation: Zika Virus
Organisms: No organisms
SOPs: ZIKV Infection Protocol
Data files: No Data files
Snapshots: No snapshots
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Studies: Viral Protein Accumulation of Zika Virus Varian...
Assays: Sample - Metadata
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Studies: Viral Protein Accumulation of Zika Virus Varian...
Assays: Sample - Metadata
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Studies: Viral Protein Accumulation of Zika Virus Varian...
Assays: Sample - Metadata
File is in .pzf format which can be opened in graphpad.
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
File is in .pzf format which can be opened in graphpad.
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Studies: Viral Protein Accumulation of Zika Virus Varian...
Assays: ZIKV infection
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Studies: Viral Protein Accumulation of Zika Virus Varian...
Assays: ZIKV attachment and entry assay
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Studies: Viral Protein Accumulation of Zika Virus Varian...
Assays: Plaque assay
Creator: John Cornelius
Submitter: John Cornelius
Investigations: Zika Virus
Abstract (Expand)
Authors: A. Y. Lu, A. Gustin, D. Newhouse, M. Jr Gale
Date Published: 31st May 2023
Publication Type: Journal
PubMed ID: 37162358
Citation: J Virol. 2023 May 31;97(5):e0198222. doi: 10.1128/jvi.01982-22. Epub 2023 May 10.