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Sample GSM419448 Query DataSets for GSM419448
Status Public on Jun 24, 2009
Title RNA from embryos of 3 groups of tnnt2 morpholino fish at 36 hpf_1
Sample type RNA
 
Source name Whole embryo
Organism Danio rerio
Characteristics strain: AB wildtype zebrafish
genetic modification: morpholino antisense tnnt2 injected
time: 36hr
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

Data table header descriptions
ID_REF
VALUE un-normalized expression level

Data table
ID_REF VALUE
AFFX-BioB-3_at 0.780359939
AFFX-BioB-5_at 2.494236633
AFFX-BioB-M_at 3.223796216
AFFX-BioC-3_at 4.193129996
AFFX-BioC-5_at 4.359235749
AFFX-BioDn-3_at 6.493865735
AFFX-BioDn-5_at 5.027303478
AFFX-CreX-3_at 8.86564649
AFFX-CreX-5_at 8.421582693
AFFX-DapX-3_at -3.038173369
AFFX-DapX-5_at -2.469426819
AFFX-DapX-M_at -6.524429386
AFFX-Dr-AB076373-1_at -2.505137467
AFFX-Dr-acta1-3_at 10.34210978
AFFX-Dr-acta1-5_at 8.9259392
AFFX-Dr-acta1-5_x_at 9.82951974
AFFX-Dr-acta1-M_at 10.04345227
AFFX-Dr-AF292559-1_at -3.309207939
AFFX-Dr-AF292559-2_s_at -2.267854891
AFFX-Dr-AF292559-3_s_at -1.775306769

Total number of rows: 15617

Table truncated, full table size 440 Kbytes.




Supplementary file Size Download File type/resource
GSM419448.CEL.gz 1.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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