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Sample GSM380428 Query DataSets for GSM380428
Status Public on Aug 31, 2010
Title Biliary Atresia Patient 47
Sample type RNA
 
Source name Human Liver Wedge Biopsy
Organism Homo sapiens
Characteristics tissue: Liver Wedge Biopsy
molecular group: Unclassified
Treatment protocol Flash Frozen
Extracted molecule total RNA
Extraction protocol RNeasy Mini Kit (QIAGEN, California, USA)
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA amplified with TargetAmp1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, WI) using both the TargetAmp t7-Oligo (dT) Primer A (Epicentre, WI) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences, CA) along with SuperScript III Reverse Transcriptase (Invitrogen, CA).
 
Hybridization protocol Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45 degC on the human HG-U133 Plus 2.0 GeneChip array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
Description Gene expression data from human liver.
Data processing The data was analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to the median of all samples.
 
Submission date Mar 15, 2009
Last update date Aug 31, 2010
Contact name Jorge A Bezerra
E-mail(s) jorge.bezerra@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Department Gastroenterology, Hepatology & Nutrition
Street address 3333 Burnet Ave.
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL570
Series (1)
GSE15235 Staging of biliary atresia at diagnosis by molecular profiling of the liver

Data table header descriptions
ID_REF
VALUE Data was RMA normalized, then normalized to the median of all samples.

Data table
ID_REF VALUE
1007_s_at 1.4788177
1053_at 1.1495411
117_at 1.2599415
121_at 1.1213694
1255_g_at 1.1359547
1294_at 0.8703919
1316_at 0.90016526
1320_at 1.1248912
1405_i_at 1.2948484
1431_at 0.66629225
1438_at 1.0123094
1487_at 0.8902933
1494_f_at 0.7530536
1598_g_at 1.3610307
160020_at 1.064289
1729_at 0.9646285
1773_at 1.1166264
177_at 1.0423648
179_at 0.9059219
1861_at 1.4097714

Total number of rows: 54675

Table truncated, full table size 1114 Kbytes.




Supplementary file Size Download File type/resource
GSM380428.CEL.gz 5.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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