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Sample GSM432331 Query DataSets for GSM432331
Status Public on Feb 01, 2010
Title SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #3
Sample type RNA
Source name SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #3
Organism Homo sapiens
Characteristics cell line: Bronchial epithelial cell line 2B4
infection: SARS-CoV-infected (MOI=0.1)
time: 12 hours post infection
Extracted molecule total RNA
Extraction protocol total RNA extraction by using an RNAqueous-4PCR kit and following the protocol recommended by the manufacturer (Ambion, Austin, TX)
Label Biotin
Label protocol According to standard Affymetrix protocol.
Hybridization protocol According to standard Affymetrix protocol.
Scan protocol According to standard Affymetrix protocol.
Description N/A
Data processing For comparison across different arrays, the data for each array were normalized by Robust Multi-chip Average (RMA) using Spotfire DecisionSite (Spotfire, Inc., Somerville, MA) and GeneSifter (VizX Labs, Seattle, WA), and probe sets with expression values below the level of background noise (as determined by detection p value) were disregarded in further analyses. Results of these analyses indicated that the RNA samples used and the data generated after the normalization were of sufficiently high quality for subsequent analyses (data not shown).
For statistical purposes, all 27 arrays were analyzed as nine separate groups (mock-, SARS-CoV-, and DHOV-infected cells at 12-, 24-, and 48-hrs). The GeneSifter-based normalization was followed by pairwise comparisons of average group values and Student's t test with Benjamini and Hochberg correction. Criteria for selection of genes were as follows: All pairwise comparisons for one group versus another (e.g., mock-versus SARS-CoV-versus DHOV-infected cells at 12 hr) were expected to be at least 1.5-fold and at least 50% greater than the fold-change observed between any two controls (e.g., mock-infected replicate 1 versus mock-infected replicate 2 at 12 hr). Exceptions were made for those probe sets that were significantly altered (fold change ≥ 1.5, p value < 0.05) at an earlier or later time point, with a magnitude that exceeded the observed fold-change between replicate controls by at least 50%. This allowed for more accurate identification of those genes that increased or decreased in expression levels over time but that fell below the stringent statistical criteria at the lower transcriptional levels. In order to ensure that results obtained from comparison of SARS-CoV- and DHOV-infected cells were specific to infection, any probe set determined to be significantly different in hybridization signal based on the above criteria was further expected to have been detected as altered (fold-change ≥ 1.5 and at least 50% greater in magnitude than any change observed between control samples, p value ≤ 0.05) between mock-infected and SARS- or DHOV-infected cells. In other words, any gene with an expression level that differed between cells infected with the two different viruses was considered as irrelevant if not altered by either virus, as determined by comparison to mock-infected control cells at that same time point.
Submission date Jul 22, 2009
Last update date Aug 28, 2018
Contact name Tomoki Yoshikawa
Organization name University of Texas Medical Branch
Street address 301 University BLVD
City Galveston
State/province TX
ZIP/Postal code 77555
Country USA
Platform ID GPL570
Series (1)
GSE17400 Dynamic Innate Immune Responses of Human Bronchial Epithelial Cells against SARS-CoV and DOHV infection
Reanalyzed by GSE119087

Data table header descriptions
VALUE RMA signal

Data table
1007_s_at 12.59041024
1053_at 8.216478307
117_at 7.811104461
121_at 11.05266072
1255_g_at 4.626309606
1294_at 7.796395327
1316_at 8.065537143
1320_at 6.922557977
1405_i_at 5.604876416
1431_at 4.998144314
1438_at 8.245307776
1487_at 9.949757564
1494_f_at 8.105642388
1552256_a_at 10.66137718
1552257_a_at 10.37805191
1552258_at 7.063919829
1552261_at 6.63889644
1552263_at 7.094872813
1552264_a_at 9.64726469
1552266_at 6.384554079

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM432331.CEL.gz 5.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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