|
| Status |
Public on Sep 17, 2013 |
| Title |
acute cellular rejection patient 3 group C |
| Sample type |
RNA |
| |
|
| Source name |
liver biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: acute cellular rejection
tissue: liver biopsy
|
| Treatment protocol |
FFPE sections and samples were processed using the FFPE RNA pure kit from Roche, following the manufacturer's protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
High Pure FFPE RNA Micro Kit ( Roche Applied Sciences) was used to extract total RNA from FFPE liver sections or slides according to manufacturers instructions
|
| Label |
biotin
|
| Label protocol |
Total RNA containing miRNA was enriched using microcon YM-100 centrifugal filter device ( Millipore Cat no: 42413,) according to the manufacturer's protocol. 100 ng of enriched RNA was labeled using Flashtag biotin RNA labeling kit ( Genisphere) according to protocol by Genisphere for labeling RNA for affymetrix Genechip RNA.
|
| |
|
| Hybridization protocol |
After labeling, 21.5 ug of RNA was hybridized for 16 hr at 48°C on GeneChip miRNA 2.0 Arrays . GeneChips were washed and stained in the Affymetrix Genechip fluidis 450 station.
|
| Scan protocol |
Hybridized samples were scanned using Genechip scanner 3000 7G (Affymetrix)
|
| Description |
archived formalin fixed histology sample
|
| Data processing |
miRNA QC Tool v1.0.33.0 , algoirthm Default was used with the following settings: Detection ( Background detection), Background adjustment (BC-CG Adjustment), Normalization (Quantile), Other Process (Add small constant, CVS tab), Other Processes (Threshhold), Summarization ( Median Polish))
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
Sep 17, 2013 |
| Contact name |
siamak salehi |
| E-mail(s) |
siamak.salehi@kcl.ac.uk
|
| Organization name |
kings college hospital
|
| Department |
liver studies
|
| Street address |
denmark hill
|
| City |
london |
| ZIP/Postal code |
se5 9rs |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL14613 |
| Series (1) |
| GSE40113 |
Distinct Micro-RNA profiles are associated with severity of hepatitis C virus recurrence and acute cellular rejection after liver transplant |
|
