|
| Status |
Public on Mar 29, 2011 |
| Title |
prdm1 mutant rep2 |
| Sample type |
RNA |
| |
|
| Source name |
prdm1 mutant, Whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
age: 25 hpf
tissue: embryo
genotype: prdm1 nulll mutant
|
| Growth protocol |
Zebrafish were maintained according to Westfield (1993) and staged by hours post fertilization (hpf) and morphology according to Kimmel (1995).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
prdm1a mutants phenotype were manually identified as wild-type or mutants. All samples contained 5 ug of carrier glycogen and were prepared using Trizol. Samples were then treated with the RiobMinusâ„¢ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Arrays were read at a resolution of 2.5-3 microns using GeneChip Scanner 3000 (Affimetrix).
|
| Data processing |
MAS 5.0
|
| |
|
| Submission date |
Mar 28, 2011 |
| Last update date |
Mar 29, 2011 |
| Contact name |
KRISTIN ARTINGER |
| E-mail(s) |
kristin.artinger@ucdenver.edu
|
| Phone |
303-724-4562
|
| Fax |
303-724-4580
|
| Organization name |
University of Colorado Denver
|
| Department |
Craniofacial Biology
|
| Street address |
12801 East 17th St
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
|
