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Sample GSM190145 Query DataSets for GSM190145
Status Public on Sep 01, 2009
Title REF52neo, bio rep 1
Sample type RNA
 
Source name REF52neo1, 2 day post-confluence
Organism Rattus norvegicus
Characteristics REF52 cells stably expressing neo gene (Clone 1)
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 7.108 55.8 A 0.32083
A03913cds_s_at 8.919 494.8 P 0.003585
A04674cds_s_at 7.851 103.1 A 0.378184
A07543cds_s_at 7.868 164.4 A 0.284747
A09811cds_s_at 8.519 19.6 A 0.988553
A16585cds_s_at 7.777 69.7 A 0.162935
A17753cds_s_at 7.617 14.6 A 0.749276
A30543cds_s_at 7.065 14.1 A 0.810313
A44407cds_at 7.708 111.7 A 0.107301
AA108277_at 6.991 157.6 P 0.002617
AA108308_i_at 6.581 5.9 A 0.96798
AA108308_s_at 10.167 489.8 A 0.162935
AA684537_at 9.728 580.4 P 0.035163
AA684929_f_at 9.106 288.6 A 0.204022
AA684960_f_at 8.985 184.8 A 0.458816
AA684963_at 10.158 911.8 P 0.001602
AA685112_at 11.041 1477.3 P 0.000219
AA685152_r_at 8.689 187 A 0.095215
AA685376_f_at 8.461 44.7 A 0.697453
AA685876_at 10.217 373.4 A 0.105738

Total number of rows: 8799

Table truncated, full table size 306 Kbytes.




Supplementary file Size Download File type/resource
GSM190145.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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