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Sample GSM190147 Query DataSets for GSM190147
Status Public on Sep 01, 2009
Title REF52neoTAg, bio rep 1
Sample type RNA
 
Source name REF52neoTAg2, 2 day post-confluence
Organism Rattus norvegicus
Characteristics REF52neo cells stably expressing SV40 Large T antigen gene (Clone 2)
Treatment protocol Cells were grown to confluence and fed with fresh medium. After two days, cells were harvested with trypsin, washed 3X with PBS-EDTA and cell pellet was frozen until RNA isolation.
Growth protocol MEM + 10% Fetal Bovine Serum + 400ug/ml G418 + Penn/Strep
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using the Ultraspec II RNA reagent (Biotex). Poly-A+ RNA was isolated from the total RNA using the Oligotex kit (Qiagen).
Label biotin
Label protocol Standard Affymetrix labeling protocol done by a Core Facility
 
Hybridization protocol Standard Affymetrix hybridization protocol done by a Core Facility
Scan protocol Standard Affymetrix scan protocol done by a Core Facility
Description Center for Applied Genomics (Newark, NJ)
Data processing Microarray Suite Version 5.0 (MAS 5.0) generated .CEL files were converted into RMA expression values using the BRB-Array Tools software (an Excel plug-in developed by Richard Simon at NCI - http://linus.nci.nih.gov/BRB-ArrayTools.html). Affymetrix Present/Absent calls and intensity values were calculated with MAS 5.0 using Affymetrix default analysis settings and global scaling with target signal = 500 as the normalization method.
 
Submission date May 17, 2007
Last update date May 29, 2009
Contact name Daniel Clark
Organization name University of Pittsburgh
Street address 3501 Terrace St.
City Pittsburgh
ZIP/Postal code 15213
Country USA
 
Platform ID GPL85
Series (2)
GSE7836 Global analysis of gene expression in REF52 cells expressing SV40 T antigens
GSE7906 Cell-type Specific Regulation of Gene Expression by Simian Virus 40 T antigens

Data table header descriptions
ID_REF
VALUE RMA expression value
MAS5 INTENSITY
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE MAS5 INTENSITY ABS_CALL DETECTION P-VALUE
A01157cds_s_at 7.088 54.6 A 0.066865
A03913cds_s_at 7.552 79.9 A 0.081337
A04674cds_s_at 7.445 47.6 A 0.52062
A07543cds_s_at 7.584 133.5 A 0.11716
A09811cds_s_at 8.099 7.2 A 0.994357
A16585cds_s_at 7.416 27.9 A 0.284747
A17753cds_s_at 7.271 3.2 A 0.824011
A30543cds_s_at 7.058 35.3 A 0.52062
A44407cds_at 7.091 36.9 A 0.35869
AA108277_at 7.912 301.1 P 0.000468
AA108308_i_at 6.473 2.4 A 0.972234
AA108308_s_at 10.212 483.8 P 0.031336
AA684537_at 9.901 417.7 P 0.024711
AA684929_f_at 8.868 187.6 A 0.138765
AA684960_f_at 8.765 41.4 A 0.541184
AA684963_at 10.894 1151.6 P 0.000266
AA685112_at 10.183 942.2 P 0.000322
AA685152_r_at 8.583 169.3 P 0.001953
AA685376_f_at 8.112 27 A 0.749276
AA685876_at 10.150 481.9 A 0.060419

Total number of rows: 8799

Table truncated, full table size 306 Kbytes.




Supplementary file Size Download File type/resource
GSM190147.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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