|
| Status |
Public on Oct 30, 2015 |
| Title |
126-Non-functional PanNET |
| Sample type |
RNA |
| |
|
| Source name |
Non-functional PanNET
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic neuroendocrine tumours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA from snap frozen tissue using 4M guanidine thiocyanate containing 0.1M 2-mercaptoethanol and centrifuged through a CsCl2 gradient. RNA quality and concentration were assesed using Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
For target preparation, 5 μg of total RNA were reverse transcribed using SuperscriptT-II/RNaseH-priming with T7-(dT)24 oligonucleotides and the second-strand cDNA synthesized using E coli DNA polymerase I. Biotinylated cRNA was generated using T7 RNA polymerase and Biotin 11-UTP.
|
| |
|
| Hybridization protocol |
10 ug of purified unfragmented target cRNA was hybridized on each chip.
|
| Scan protocol |
The microarrays were hybridized, washed, and processed using a direct detection method of the biotin-containing transcripts by a Streptavidin-Alexa647 conjugate (Invitrogen, Carlsbad, CA). Scanned images were analyzed using the Genepix 6.0 software (Axon Instruments, Sunnyvale, CA).
|
| Description |
Q5
|
| Data processing |
The chip was annotated using AnnBuilder Package available for the R software starting from the GeneBank accession numbers made available through Compugen/Sigma-Genosys.
The median signal subtracted for the background was normalized using a variance-stabilizing transformation stratifying the spots by grid (Huber W, von Heydebreck A, Sultmann H, et al: Bioinformatics 18:S96-S104, 2002 [suppl 1]) as implemented in the vsn package.
|
| |
|
| Submission date |
Sep 22, 2015 |
| Last update date |
Oct 30, 2015 |
| Contact name |
Anguraj Sadanandam |
| E-mail(s) |
anguraj.sadanandam@icr.ac.uk
|
| Organization name |
Institute of Cancer Research (ICR), London
|
| Department |
Molecular Pathology
|
| Lab |
Systems and Precision Cancer Medicine Team
|
| Street address |
15 Cotswold Road
|
| City |
Sutton |
| State/province |
Surrey |
| ZIP/Postal code |
SM2 5NG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20945 |
| Series (1) |
| GSE73338 |
Pancreatic endocrine tumours: expression profiling evidences a rold for AKT-mTOR pathway |
|
