|
| Status |
Public on Feb 17, 2006 |
| Title |
Zebrafish_Wild Type_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
wild type embryos, 9 hours post fertilization
|
| Organism |
Danio rerio |
| Characteristics |
TLAB wild type embryos collected 9 hour post fertilization
|
| Biomaterial provider |
Antonio Giraldez/Alex Schier
|
| Growth protocol |
embryos were collected and grown in egg water (Stock salts: 40 g "Instant Ocean" Sea Salts added to 1 L distilled water
Egg water = 1.5 ml stock salts added to 1 L distilled water = 60 µg/ml final concentration) at 28 degrees Celcius prior to RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 20 embyros using Trizol (Invitrogen). 20-50 ng of sample was quality checked using the RNA 6000 NanoAssay and Bioanalyzer 2100 (Agilent). Samples with a 28S/18S ribosomal peak ratio of 1.8-2.0 were labled.
|
| Label |
biotin
|
| Label protocol |
2 micrograms of total RNA was used for cDNA synthesis using an oligo(dT)-T7 primer and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Synthesis, linear amplification, and labeling of cRNA were accomplished by in vitro transcription using the MessageAmp aRNA Kit (Ambion) and biotinylated nucleotides(Enzo Diagnostics).
|
| |
|
| Hybridization protocol |
10 micrograms of labeled and fragmented cRNA were hybridized to GeneChip at 45 degrees C for 16 hours. Post hybridization staining and washing were performed according to the manufacturer (Affymetrix).
|
| Scan protocol |
GeneChips were scanned with a high-numerical Aperture and flying objective (FOL) lens in a GS3000 scanner (Affymetrix).
|
| Description |
--
|
| Data processing |
normalization of all arrays was performed by dChip v.3.1. The values were then calculated using dChip's PM/MM difference model (www.dchip.org)
|
| |
|
| Submission date |
Feb 05, 2006 |
| Last update date |
Jun 03, 2013 |
| Contact name |
Antonio J. Giraldez |
| E-mail(s) |
antonio.giraldez@yale.edu
|
| Phone |
203 785 5423
|
| Organization name |
Yale University
|
| Department |
Genetics
|
| Lab |
Giraldez Lab
|
| Street address |
333 Cedar Street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE4201 |
Zebrafish microRNA miR-430 promotes deadenylation and clearance of maternal mRNAs |
|
