|
| Status |
Public on May 04, 2018 |
| Title |
TOP-IBK-60_T30 |
| Sample type |
RNA |
| |
|
| Source name |
Kidney Biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
gender: f
age: 86
last donor creatinine: 0.70
tissue: Kidney Biopsy
|
| Treatment protocol |
Renal wedge biopsies were stored in RNALater (Quiagen) immediately after removal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using miRNeasy (Quiagen) following the manufacturers protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer, and only samples with a A260/280 ratio of >1.6 were used.
|
| Label |
Cy3
|
| Label protocol |
From each biopsy 200 ng of total RNA was used to generate Cyanine 3 (Cy3) labelled cRNA for hybridisation to Agilent oligonucleotide microarrays according to the Agilent One-Color Microarray protocol (Agilent Technologies, Santa Clara, CA, USA). Briefly, first and second strands of cDNA were generated containing a T7 RNA polymerase promoter using the Agilent Quick Amp Kit. A T7 RNA polymerase synthesized cRNA and incorporated Cy3-labelled CTP. Labelled cRNA was purified on Qiagen RNeasy columns and the final cRNA concentration and labeling efficiency were determined using a Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE, USA).
|
| |
|
| Hybridization protocol |
For each sample 1.65 ug cRNA was fragmented and hybridized to an Agilent Human Whole Genome 44K oligoarray for 17 hours at 65oC.
|
| Scan protocol |
Arrays were washed and scanned at 5 um using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA), and signal intensity data was extracted using Agilent Feature Extraction software (v10.5.1).
|
| Data processing |
Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.
|
| |
|
| Submission date |
Feb 17, 2017 |
| Last update date |
May 06, 2018 |
| Contact name |
Johannes Leierer |
| Organization name |
Medical University Innsbruck
|
| Department |
Internal Medicine IV - Nephrology
|
| Street address |
Anichstr. 35
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE95026 |
Validation of systems biology derived molecular markers of donor organ status associated with long term allograft function |
|
