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Sample GSM1163479 Query DataSets for GSM1163479
Status Public on Jul 30, 2013
Title SHAE003_Mock_0hr_2
Sample type RNA
 
Source name SHAE003_Mock_0hr_2
Organism Homo sapiens
Characteristics cell type: Human airway epithelium cells (HAE)
infection code: Mock
sample material: cells
timepoint: 0hr
biological replicate: 2
Treatment protocol Cells were seeded in 6-well plates (1 x 10e6 cells/well) two days prior to infection. Immediately preceding infection, cell monolayers were washed with fresh medium and inoculated with either SARS viruses or A/CA/04/2009 at an MOI of 2 and subsequently incubated at 37°C for 40 minutes. Mock-infected controls were inoculated with culture medium only. Following the incubation, cell monolayers were washed 3X with 1X PBS and fresh medium was added to the wells prior to time 0.
Growth protocol Human airway epithelium cultures (HAE) were generated by provision of an air-liquid interface for 6 to 8 weeks to form well-differentiated , polarized cultures that resemble in vivo pseudo-stratified mucociliary epithelium.
Extracted molecule total RNA
Extraction protocol At 0, 12, 24, 36, 48, 60, 72, 84 and 96 hours post-infection (hpi) (SARS-CoV virus), 0, 24, 48, 60, 72, 84 and 96 hours post-infection (hpi) (SARS ddORF6 and BatSRBD viruses) or 0, 6, 12, 18, 24, 36 and 48 hpi (H1N1) triplicate/quadruplicate wells of infected cells or mock infected were washed with 1X PBS and lysed directly with 1 ml of Trizol (Invitrogen) according to the manufacturer’s recommendation. The resulting lysates were stored at -80°C until further processing. 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 quantitative PCR (qPCR) and microarray analyses.
Label Cy3
Label protocol The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.
 
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 human HG (Design ID 014850) 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. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
 
Submission date Jun 14, 2013
Last update date Jul 31, 2013
Contact name Michael Katze
E-mail(s) [email protected]
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 GPL6480
Series (2)
GSE47961 SHAE003: SARS-CoV, SARS-dORF6 and SARS-BatSRBD infection of HAE cultures.
GSE47963 SARS-CoV, SARS-dORF6 and SARS-BatSRBD infection of HAE cultures.

Data table header descriptions
ID_REF
VALUE gProcessedSignal

Data table
ID_REF VALUE
A_23_P100001 9.739873515
A_23_P100011 6.472370687
A_23_P100022 4.921691129
A_23_P100056 3.592618816
A_23_P100074 10.02753682
A_23_P100092 7.441169719
A_23_P100103 7.134116383
A_23_P100111 7.325290797
A_23_P100127 6.422863307
A_23_P100133 7.621971249
A_23_P100141 8.194400803
A_23_P100156 8.559779584
A_23_P100177 7.316474144
A_23_P100189 6.384111927
A_23_P100196 10.92926413
A_23_P100203 11.85427499
A_23_P100220 12.28884915
A_23_P100240 3.360231821
A_23_P10025 5.326321193
A_23_P100263 11.79534045

Total number of rows: 33421

Table truncated, full table size 801 Kbytes.




Supplementary file Size Download File type/resource
GSM1163479_US23502418_251485073223_S01_GE1_107_Sep09_1_3.txt.gz 8.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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