|
| Status |
Public on Apr 01, 2009 |
| Title |
IPC at preimplantation, 1 |
| Sample type |
RNA |
| |
|
| Source name |
Donor hepatic allograft following ischemic preconditioning at pre-implantation time point
|
| Organism |
Homo sapiens |
| Characteristics |
recipient gender: Female
recipient age: 57
recipient ethnicity: White
tissue: Liver
protocol: IPC at pre-implantation
|
| 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 pre-implantation time point
|
| 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 |
|
