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Sample GSM758841 Query DataSets for GSM758841
Status Public on Jun 21, 2012
Title Vero E6 SARS CoV DeltaE 15hpi rep3
Sample type RNA
 
Source name Vero E6 cells, infected with SARS-CoV-DeltaE, 15hpi
Organism Chlorocebus aethiops
Characteristics infection: SARS CoV DeltaE
cell line: Vero E6
induce ifnβ: NO
hours post infection: 15 hpi
Growth protocol Subconfluent monolayers (90% confluency) of Vero E6 and MA-104 cells were infected at multiplicity of infection (moi) of 0.01 or 2 with the viruses rSARS-CoV-ΔE, and rSARS-CoV or rSARS-CoV-MA15-ΔE and rSARS-CoV-MA15. Culture supernatants were collected at different hours post-infection (hpi) and virus titer was determined as previously described.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer´s instructions. RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies).
Label biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix GeneChips (Human Genome U133 plus 2.0) at 45ºC during 16 hours. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, 20mM of EDTA and 0,01% tween-20
Scan protocol The arrays were stained with streptavidin-ficoeritrin and read at 1.56 μm in a GeneChip Scanner 3000 7G System (Affymetrix, Santa Clara, CA)
Description Gene expression data from Vero E6 cells infected with SARS-CoV-DeltaE and collected at 15hpi
Data processing GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.
 
Submission date Jul 12, 2011
Last update date Jun 21, 2012
Contact name Juan Carlos Oliveros
Organization name CNB, CSIC
Street address Darwin 3
City Cantoblanco
State/province Madrid
ZIP/Postal code 28049
Country Spain
 
Platform ID GPL570
Series (1)
GSE30589 Severe acute respiratory syndrome coronavirus envelope protein regulates cell stress responses and apoptosis

Data table header descriptions
ID_REF
VALUE Log2 RMA signal

Data table
ID_REF VALUE
1007_s_at 6.67
1053_at 5.19
117_at 6.36
121_at 8.48
1255_g_at 3.98
1294_at 5.96
1316_at 6.27
1320_at 4.99
1405_i_at 3.93
1431_at 4.97
1438_at 5.89
1487_at 6.7
1494_f_at 5.74
1552256_a_at 5.79
1552257_a_at 6.8
1552258_at 5.14
1552261_at 4.93
1552263_at 3.65
1552264_a_at 6.54
1552266_at 4.21

Total number of rows: 54675

Table truncated, full table size 838 Kbytes.




Supplementary file Size Download File type/resource
GSM758841_E-3_15hpi.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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