|
| Status |
Public on Jun 24, 2009 |
| Title |
RNA from embryos of 3 groups of tnnt2 morpholino fish at 48 hpf_3 |
| Sample type |
RNA |
| |
|
| Source name |
Whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB wildtype zebrafish
genetic modification: morpholino antisense tnnt2 injected
time: 48hr
|
| Treatment protocol |
One cell zebrafish embryos were injected with morpholino antisense against control or cardiac troponin t2 (from Gene-tools). Whole embryo RNA was extracted at 32, 48, and 60h post fertilization and transcriptionally profiled. Groups contained equal numbers of embryos from each parent pair.
|
| Growth protocol |
Embryos were incubated in E3 medium at 28 degrees celsius according to standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Trizol (Invitrogen) method following manufacturer’s instructions. Trizol-purified RNA was then treated with RNase-free DNase I (Roche) and purified with RNeasy spin columns (Qiagen). RNA quantity and quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| 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 Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned at 3-mm density with a GeneChip® Scanner 3000 7G 4C (Affymetrix).
|
| Description |
gene expression from whole zebrafish embryo
|
| Data processing |
The data were analyzed using the PUMA package, Propagating Uncertainty in Microarray data (www.bioconductor.org). Fold change cut-off was set at 1 in the log2 scale. Cut-off of probability of positive ratio for the analysis of differentially expressed genes was set at 0.90.
|
| |
|
| Submission date |
Jun 22, 2009 |
| Last update date |
Jun 23, 2009 |
| Contact name |
Marta Milo |
| E-mail(s) |
m.milo@sheffield.ac.uk
|
| Organization name |
University of Sheffield
|
| Department |
Biomedical Science
|
| Street address |
Western Bank
|
| City |
Sheffield |
| State/province |
South Yorkshire |
| ZIP/Postal code |
S10 2TN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE16740 |
The effect of cardiac troponin T2 knockdown on gene expression in zebrafish embryos |
|
