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Status |
Public on Oct 13, 2011 |
Title |
zebrafish_SB_4.3h_2 |
Sample type |
RNA |
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Source name |
4.3-hpf SB-treated zebrafish embryos
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Organism |
Danio rerio |
Characteristics |
subtype: Sb morphant development hour: 4.3 hpf
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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.
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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.
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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
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Label |
biotin
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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).
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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.
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Scan protocol |
Chip images were scanned with GeneChip® Scanner 3000 and converted to raw data with the GCOS 1.4 software.
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Description |
experiment 1
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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).
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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
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City |
Shanghai |
ZIP/Postal code |
200235 |
Country |
China |
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|
Platform ID |
GPL1319 |
Series (1) |
GSE32914 |
Study of Mid-Blastula Transition of zebrafish embryos |
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