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Status |
Public on Jun 24, 2009 |
Title |
RNA from embryos of 3 groups of tnnt2 morpholino fish at 60 hpf_2 |
Sample type |
RNA |
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Source name |
Whole embryo
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Organism |
Danio rerio |
Characteristics |
strain: AB wildtype zebrafish genetic modification: morpholino antisense tnnt2 injected time: 60hr
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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.
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Growth protocol |
Embryos were incubated in E3 medium at 28 degrees celsius according to standard protocols.
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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).
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Label |
biotin
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Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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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.
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Scan protocol |
GeneChips were scanned at 3-mm density with a GeneChip® Scanner 3000 7G 4C (Affymetrix).
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Description |
gene expression from whole zebrafish embryo
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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.
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Submission date |
Jun 22, 2009 |
Last update date |
Jun 23, 2009 |
Contact name |
Marta Milo |
E-mail(s) |
m.milo@sheffield.ac.uk
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Organization name |
University of Sheffield
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Department |
Biomedical Science
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Street address |
Western Bank
|
City |
Sheffield |
State/province |
South Yorkshire |
ZIP/Postal code |
S10 2TN |
Country |
United Kingdom |
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Platform ID |
GPL1319 |
Series (1) |
GSE16740 |
The effect of cardiac troponin T2 knockdown on gene expression in zebrafish embryos |
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