|
| Status |
Public on Sep 01, 2013 |
| Title |
MycRas_5 |
| Sample type |
RNA |
| |
|
| Source name |
tumor tissue from LT2/MYC/RAS mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain background: FVB
genotype/variation: MYC-RAS over-expressor
tissue: liver tumor
|
| Treatment protocol |
Doxycycline chow was replaced with regular chow to switch on oncogene expression
|
| Growth protocol |
Mice were kept on doxy diet to keep oncogenes switched off
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using mirVANA kit from Ambion. The miRNA-enriched fraction of small RNAs was purified from total RNA by polyacrylamide gel electrophoresis using Ambion’s flashPAGE™ kits, Ambion Inc., Austin, TX.
|
| Label |
biotin
|
| Label protocol |
The 3’ ends of the RNA molecules were tailed and biotin-labeled using the mirVana™ miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit’s dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).
|
| |
|
| Hybridization protocol |
Hybridization, washing, staining, imaging, and signal extraction were performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.
|
| Scan protocol |
The fluorecence data is extracted at 1.4 micron pixel resolution using the Affymetrix 3000 7G scanner.
|
| Description |
A0009919: MYC-RAS over-expressor
|
| Data processing |
The signal processing implemented is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes.
For statistical hypothesis testing, a two-sample t-Test, with assumption of equal variance, was applied. One-way ANOVA was used. These tests define which probes are considered to be significantly differentially expressed, or significant, based on a default p-value of 0.05 and log2 difference > 1. The post-normalized data scale is reported as generalized log2 data.
|
| |
|
| Submission date |
Feb 22, 2013 |
| Last update date |
Sep 01, 2013 |
| Contact name |
Andrei Goga |
| E-mail(s) |
andrei.goga@ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Cell & Tissue Biology
|
| Lab |
Goga Lab
|
| Street address |
513 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0512 |
| Country |
USA |
| |
|
| Platform ID |
GPL16713 |
| Series (1) |
| GSE44570 |
miRNA expression changes in murine liver tumorigenesis |
|
