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Sample GSM142321 Query DataSets for GSM142321
Status Public on Oct 25, 2007
Title MO control zebrafish embryo 21hpf-2
Sample type RNA
 
Source name Control MO injected Danio rerio embryo, 21 hours post-fertilization
Organism Danio rerio
Characteristics strain: TL;
age: 21 hours post-fertilization;
Biomaterial provider Tokyo Institue of Technology
Treatment protocol Embryos were injected at the one-cell or two-cell stages with approximately 2.5 pmol of commercially available standard control morpholino oligo with a 3’ carboxyfluorescein (Gene Tools, LLC).
Growth protocol Embryos were maintained in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4) at 28.5 centigrade for 21 hours post-fertilization.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from embryos using Sepasol-RNA I super (Nacalai tesque), followed by further purification using an RNeasy mini protocol for RNA cleanup (Qiagen).
Label biotin
Label protocol In vitro synthesis of cDNA and target cRNA preparations were carried out with 5 µg of total RNA according to a One-Cycle Target Labeling protocol (Affymetrix). Label reaction was performed using the GeneChip IVT Labeling Kit.
 
Hybridization protocol Aliquots of cRNA (20 µg) of each sample were fragmented, hybridized to the Genechip Zebrafish Genome Array, and processed according to the manufacturer’s instructions.
Scan protocol Fluidics Station 400 is used to wash and stain the probe arrays, and controlled by Affymetrix® Microarray Suite. The scanner is also controlled by Affymetrix® Microarray Suite. All the procedure was according to the manufacturer’s instructions.
Description A High-Resolution Transcriptome Map of the Control Morpholino Oligo Injected Zebrafish Embryo
Data processing Scanned data were analyzed with the GC-RMA algorithm (REF) to estimate gene expression levels.
 
Submission date Oct 25, 2006
Last update date Oct 25, 2006
Contact name Tadashi Wada
E-mail(s) wada.t.ac@m.titech.ac.jp
Phone +81-45-924-5798
Fax +81-45-924-5834
URL http://www.handa.bio.titech.ac.jp/
Organization name Tokyo Institute of Technology
Department Bioscience and Biotechnology
Lab The lab of Dr. HANDA Hiroshi and Dr. WADA Tadashi
Street address 4259 Nagatsuta-cho, Midori-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 226-8503
Country Japan
 
Platform ID GPL1319
Series (1)
GSE6127 The expression of Spt5 targeted genes

Data table header descriptions
ID_REF
VALUE means Signal of the array feature
ABS_CALL means Detection of the array feature
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 61.9 P 0.001796
AFFX-BioB-M_at 55.3 P 0.000127
AFFX-BioB-3_at 32.7 P 0.018281
AFFX-BioC-5_at 162.1 P 0.00006
AFFX-BioC-3_at 135.5 P 0.000044
AFFX-BioDn-5_at 344.4 P 0.000044
AFFX-BioDn-3_at 643.7 P 0.000081
AFFX-CreX-5_at 1714.2 P 0.000044
AFFX-CreX-3_at 2870.7 P 0.000044
AFFX-DapX-5_at 89.9 P 0.00011
AFFX-DapX-M_at 165.7 P 0.000662
AFFX-DapX-3_at 206.6 P 0.000044
AFFX-LysX-5_at 16.7 P 0.006187
AFFX-LysX-M_at 35.1 P 0.028457
AFFX-LysX-3_at 52.1 P 0.000225
AFFX-PheX-5_at 19 P 0.003595
AFFX-PheX-M_at 4.7 A 0.313723
AFFX-PheX-3_at 49.5 P 0.000857
AFFX-ThrX-5_at 32.3 P 0.005565
AFFX-ThrX-M_at 29.2 P 0.000446

Total number of rows: 15617

Table truncated, full table size 497 Kbytes.




Supplementary file Size Download File type/resource
GSM142321.CEL.gz 3.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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