|
| Status |
Public on Jan 06, 2012 |
| Title |
db/db mouse sample 402 |
| Sample type |
RNA |
| |
|
| Source name |
8 week db/db mouse sciatic nerve
|
| Organism |
Mus musculus |
| Characteristics |
strain: BKS
genotype/variation: db/db
age: 8 weeks
tissue: sciatic nerve
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from sciatic nerve using a commercially available silica gel-based isolation protocol (RNeasy Mini Kit, QIAGEN Inc., Valencia, CA) including an on-column DNase digestion following the manufacturer's protocol. RNA quantity and quality was measured by microfluid electrophoresis using the RNA 6000 Pico LabChip® on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
Of the total RNA, 75 ng from each sample was amplified and biotin-labeled using the Ovation™ Biotin-RNA Amplification and Labeling System (NuGEN Technologies Inc., San Carlos, CA) according to the manufacturer’s protocol
|
| |
|
| Hybridization protocol |
Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
|
| Description |
Feldman_402.CEL
Gene expression data from 8 week db/db mouse sciatic nerve
|
| Data processing |
The Affymetrix CEL files were initially analyzed using a local version of the GenePattern genomic analysis platform from the Broad Institute. The samples were Robust Multi-array Average (RMA) normalized using the BrainArray Custom CDF version 12. Since the RNA amplification and hybridization was performed in two batches, normalized, log2 transformed expression values from the two batches of microarrays were adjusted for batch effect bias using the Distance Weighted Discrimination (DWD) batch effect correction method.
|
| |
|
| Submission date |
Jan 05, 2012 |
| Last update date |
Jan 06, 2012 |
| Contact name |
Manjusha Pande |
| E-mail(s) |
mpande@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
BRCF
|
| Lab |
Bioinformatics Core
|
| Street address |
2800 Plymouth Rd.
|
| City |
Ann Arobr |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL9746 |
| Series (1) |
| GSE34889 |
Molecular Mechanisms of Diabetic Neuropathy: A Transcriptional Profling Study of db/db Mouse Sciatic Nerve |
|
