|
| Status |
Public on Feb 13, 2018 |
| Title |
Mock_B314_36h_2 |
| Sample type |
RNA |
| |
|
| Source name |
Nasal Epithelial Cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Nasal Epithelial Cells
infection: Mock
sampleID: B314
timepoint: 36h
|
| Treatment protocol |
Differentiated hNECs where infected at a multiplicity of infection (MOI) of 5 50% tissue culture infectious dose per cell. All incubations were performed at 32oC in a humidified environment with 5% CO2. Prior to infection, cells were apically washed with 200 μl DMEM (supplemented with 0.3% BSA, 2mM Glutamax, 100 U/ml Penicillin, and 100 µg/ml Streptomycin) and the basolateral media was refreshed with 500 μl of fresh LHC Basal Medium:DMEM-H. The virus inoculum was added to the apical compartment in a volume of 100 μl and incubated for 2 hours, after which the inoculum was aspirated and the apical chamber was washed three times with 200 μl phosphate buffered saline containing calcium and magnesium (PBS+). The plates were then returned to the incubator. Both apical washes and basolateral medium were collected and stored at -70oC. Virus production each time point was quantified by limited dilution infection of MDCKs using apical wash samples. The TCID50 for each sample was calculated using the Reed-Muench algorithm (Reed, 1938). RNA was isolated from Trizol homogenates from samples harvested at 24hpi and 36hpi.
|
| Growth protocol |
Human nasal epithelial cells (hNECs) were obtained from non-diseased hosts during endoscopic sinus surgery for non-infection related conditions and grown in culture at the air-liquid interface (ALI) as previously described (Lane et al., 2004; Ramanathan and Lane, 2007; Ramanathan et al., 2007). Tissue processing, differentiation medium, and culture conditions have been previously described in detail (Fischer et al., 2015). Seasonal influenza A virus A/Victoria/361/2011 (H3N2) and an antigenically-matched live attenuated influenza vaccine virus (LAIV; WT HA and NA, all other proteins from A/Ann Arbor/6/1960) were utilized in this study. Viral seed stocks were obtained from Medimmune.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.
|
| Label |
Cy3
|
| Label protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.
|
| Scan protocol |
Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.
|
| Data processing |
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
|
| |
|
| Submission date |
Jun 10, 2016 |
| Last update date |
Feb 13, 2018 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Michael G. Katze, Ph.D
|
| Street address |
Rosen Building 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE83215 |
Evaluation of the immunogenicity of live-attenuated influenza vaccines in nasal epithelial cells in primary differentiated human nasal epithelial cells [Microarray Expression] |
| GSE83285 |
Evaluation of the immunogenicity of live-attenuated influenza vaccines in nasal epithelial cells in primary differentiated human nasal epithelial cells |
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