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Sample GSM1163412 Query DataSets for GSM1163412
Status Public on Jul 30, 2013
Title SHAE003_BAT_72hr_3
Sample type RNA
 
Source name SHAE003_BAT_72hr_3
Organism Homo sapiens
Characteristics cell type: Human airway epithelium cells (HAE)
infection code: BatSRBD
sample material: cells
timepoint: 72hr
biological replicate: 3
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 10.32468859
A_23_P100011 6.737747259
A_23_P100022 4.232743731
A_23_P100056 5.070014752
A_23_P100074 9.465917557
A_23_P100092 7.332319836
A_23_P100103 7.076154763
A_23_P100111 7.492122428
A_23_P100127 5.852897705
A_23_P100133 7.421744642
A_23_P100141 7.138450415
A_23_P100156 8.437459923
A_23_P100177 7.889661759
A_23_P100189 5.936371976
A_23_P100196 10.91962517
A_23_P100203 11.84099709
A_23_P100220 12.21230849
A_23_P100240 3.434949972
A_23_P10025 4.126247459
A_23_P100263 13.41261812

Total number of rows: 33421

Table truncated, full table size 801 Kbytes.




Supplementary file Size Download File type/resource
GSM1163412_US23502418_251485073280_S01_GE1_107_Sep09_1_4.txt.gz 8.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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