|
| Status |
Public on Nov 01, 2012 |
| Title |
Metabolic memory 0h rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Caudal fin of Danio rerio
|
| Organism |
Danio rerio |
| Characteristics |
disease state: Metabolic memory
time (post amputation): 0h
tissue: caudal fin
|
| Treatment protocol |
Fish were anesthetized by placing them in 1:1000 2-phenoxyethanol for 1-2 minutes. 0.3% streptozocin solution in 5mM citrate buffer, pH 5.0 to a dose of 350 mg/kg was injected in the dorsal half of the fin with a PLI-90 injector (Harvard Biosciences, Inc., MA). The drug was injected on days 1,3,5, 12 and 19 of the experiment. This was followed by 60 days of keeping the fish without the drug. Control fish were injected with a like volume of citrate buffer.
|
| Growth protocol |
Wild-type zebrafish were maintained under standard laboratory conditions using a light schedule of 14 h on and 10 h off at a temperature of 28.5°C. Fish were fed twice daily using a combination of dry food and brine shrimp.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each time point, triplicate samples from 15 caudal fins were collected and immediately placed into Triazol. The samples were homogenizedand then centrifuged. The RNA was extracted from the supernatant using the purelink RNA mini-kit (Life Technologies Corporation, Carlsbad, CA) according to the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the GeneChip® Scanner 3000 7G
|
| Description |
Gene expression data from regenerating caudal fin of Danio rerio
|
| Data processing |
The data were analyzed with Partek GS 6.5 software (St. Louis, MO) using GCRMA normalization algorithm
|
| |
|
| Submission date |
Apr 11, 2012 |
| Last update date |
Nov 01, 2012 |
| Contact name |
Alexey Aleksandrovich Leontovich |
| E-mail(s) |
leontovich.alexey@mayo.edu
|
| Phone |
507-284-4850
|
| Organization name |
Mayo Clinic
|
| Department |
Health Science Research
|
| Lab |
Biomedical Statistics and Informatics
|
| Street address |
200 First street
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55902 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (2) |
| GSE37163 |
Gene expression data from time course of fin regeneration in Danio rerio (part 1) |
| GSE37165 |
Gene expression data from time course of fin regeneration in Danio rerio |
|
