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Sample GSM388409 Query DataSets for GSM388409
Status Public on Apr 01, 2009
Title IPC at post-reperfusion, 5
Sample type RNA
 
Source name Donor hepatic allograft following ischemic preconditioning at post-reperfusion
Organism Homo sapiens
Characteristics recipient gender: Male
recipient age: 57
recipient ethnicity: Asian
tissue: Liver
protocol: IPC at post-reperfusion
Treatment protocol Hepatic ischemic preconditioning was administered in the donor and consisted of hilar inflow occlusion for 10 minutes followed by reperfusion until circulatory arrest. Donor graft biopsies were performed at two time points: one immediately before commencement of implantation in the recipient and another at 90 minutes following reperfusion with portal blood. The remainder of the liver procurement and transplantation protocols in the donor and recipient were as per standard of practice.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from hepatic tissue using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA, # 74104) according to the manufacturer’s protocol.
Label biotin
Label protocol cRNA end-labeled with biotin was prepared according to the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay Manual Version 4 from 300 ng total RNA (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).
 
Hybridization protocol The biotin labeled cDNA was hybridized to the Human Gene 1.0 ST Array for 16 hours at 45ºC using the GeneChip Hybridization Oven 640 (Affymetrix, Santa Carla, CA, USA, #800138). Washing and staining with streptavidin-phycoerythrin was performed using the GeneChip Fluidics Station 450 (Affymetrix, Santa Carla, CA, USA, # 00-0079).
Scan protocol Images were acquired using the Affymetrix Scanner 3000 7G Plus (Affymetrix, Santa Carla, CA, USA, # 00-0210).
Description Gene expression data from hepatic allograft following ischemic preconditioning at post-reperfusion
Data processing Fluorescence intensities captured by the Affymetrix Scanner were converted to numerical values using the Affymetrix GeneChip Operating Software version 1.0. These values were subjected to a log2 transformation and were then standardized using quantile normalization with the Robust Multi-array Analysis (RMA) algorithm. Gene expression values were median centered and then imported into the Multiple Experiment Viewer (MEV 4.0) software. Principal Component Analysis was performed to check consistency of the experiments to determine if there were any chip outliers. Significant transcripts were selected using a t-test with p values less than 0.05.
 
Submission date Mar 31, 2009
Last update date Mar 31, 2009
Contact name Ali Raza
E-mail(s) razaal@umdnj.edu
Phone 973-972-6156
Fax 973-972-6803
Organization name UMDNJ
Department Surgery
Lab Baburao Koneru
Street address 185 South Orange Ave
City Newark
State/province NJ
ZIP/Postal code 07102
Country USA
 
Platform ID GPL6244
Series (1)
GSE15480 Global Gene Expression in Deceased Donor Liver Transplantation with Ischemic Preconditioning

Data table header descriptions
ID_REF
VALUE log2 transformed signal

Data table
ID_REF VALUE
7892501 2.215128
7892502 3.770213
7892503 2.465318
7892504 9.427032
7892505 2.43219
7892506 2.768543
7892507 3.399677
7892508 3.467457
7892509 10.92104
7892510 1.891674
7892511 2.336252
7892512 5.506739
7892513 3.151922
7892514 9.933866
7892515 8.992967
7892516 3.631917
7892517 3.073971
7892518 1.939027
7892519 5.105459
7892520 9.293165

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.




Supplementary file Size Download File type/resource
GSM388409.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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