|
| Status |
Public on Sep 24, 2010 |
| Title |
non-progressive sural nerve, patient 7 |
| Sample type |
RNA |
| |
|
| Source name |
non-progressive DN sural nerve 52 weeks
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: sural nerve
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from a 1 cm segment of each sural nerve biopsy using a commercially available kit (RNeasy Mini Kit; QIAGEN, Inc., Valencia, CA), including an on-column deoxyribonuclease digestion and following the manufacturer’s protocol. RNA quality and quantity were assessed by microfluid electrophoresis using an RNA 6000 Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the Nugen Ovation V2 kit protocol from 75 ng total RNA (Ovation RNA Amplification System V2 Manual, 2007, NuGEN).
|
| |
|
| 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 |
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
| 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 HGU133Plus2_Hs_ENTREZG version 12. Cyber-T and ChipInspector (Genomatix, Germany) were used to analyze the expression data.
|
| |
|
| Submission date |
Sep 23, 2010 |
| Last update date |
Sep 23, 2010 |
| Contact name |
Junguk Hur |
| E-mail(s) |
junguk.hur@med.und.edu
|
| Organization name |
University of North Dakota
|
| Department |
Biomedical Sciences
|
| Street address |
1301 N. Columbia Rd. Stop 9037
|
| City |
Grand Forks |
| State/province |
ND |
| ZIP/Postal code |
58202-9037 |
| Country |
USA |
| |
|
| Platform ID |
GPL10526 |
| Series (1) |
| GSE24290 |
Sural nerve of progressive and non-progressive diabetic neuropathy patients |
|
