|
| Status |
Public on Oct 13, 2011 |
| Title |
zebrafish_SB_4.3h_3 |
| Sample type |
RNA |
| |
|
| Source name |
4.3-hpf SB-treated zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
subtype: Sb morphant
development hour: 4.3 hpf
|
| Treatment protocol |
Sequence for Sb MO was designed complementary to the intron-exon junction: 5’- ACATTTGACTGTGGAGAGGAAAAAA-3’ (Gene Tools). Morpholinos were diluted to the desired concentration in nuclease free water and injected at the 1-2 cell stage.
|
| Growth protocol |
Fertilized zebrafish embryos, treated or non-treated, were allowed to develop in natural conditions and harvested at a particular time (a certain hour post fertilization) for gene expression profiling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from culture samples by using sing the Trizol reagent (Gibco BRL, Cleveland, OH) and further purified with the RNeasy mini kit (QIAGEN, P/N 74104) according to standard protocols
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNAs weighted 23.3-35.0 ug (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
hybridizations were carried out in Hybridization Oven 640 (Affymetrix, 800139 (220V)) using the GeneChip® Hybridization, Wash and Stain Kit, Affymetrix, P/N 900720.
|
| Scan protocol |
Chip images were scanned with GeneChip® Scanner 3000 and converted to raw data with the GCOS 1.4 software.
|
| Description |
experiment 1
|
| Data processing |
The CEL-format expression data were read into the R computing environment (‘ReadAffy’ of the ‘affy’ package [6]) and normalized with the Robust Multichip Average method (‘rma’ of the ‘affy’ package).
|
| |
|
| Submission date |
Oct 12, 2011 |
| Last update date |
Oct 13, 2011 |
| Contact name |
Hui Yu |
| E-mail(s) |
yuhui@scbit.org
|
| Organization name |
Shanghai Center for Bioinformation Technology
|
| Street address |
No.100, Rd. Qinzhou
|
| City |
Shanghai |
| ZIP/Postal code |
200235 |
| Country |
China |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE32914 |
Study of Mid-Blastula Transition of zebrafish embryos |
|
