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Sample GSM142316 Query DataSets for GSM142316
Status Public on Oct 25, 2007
Title Untreated zebrafish embryo 5hpf-1
Sample type RNA
 
Source name Danio rerio embryo, 5 hours post-fertilization
Organism Danio rerio
Characteristics strain: TL
age: 5 hours post-fertilization
Biomaterial provider Tokyo Institue of Technology
Treatment protocol non-treatment
Growth protocol maintained in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4) at 28.5 centigrade 5 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 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 mean signal of the array feature
ABS_CALL mean detection of the array feature
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 55.8 P 0.000446
AFFX-BioB-M_at 51.5 P 0.000081
AFFX-BioB-3_at 37.5 P 0.000581
AFFX-BioC-5_at 137.5 P 0.00007
AFFX-BioC-3_at 95.2 P 0.000052
AFFX-BioDn-5_at 176.8 P 0.000044
AFFX-BioDn-3_at 648 P 0.000044
AFFX-CreX-5_at 1343.8 P 0.000044
AFFX-CreX-3_at 2504.3 P 0.000044
AFFX-DapX-5_at 52.5 P 0.00011
AFFX-DapX-M_at 99.3 P 0.000095
AFFX-DapX-3_at 121.3 P 0.00006
AFFX-LysX-5_at 7.9 P 0.005565
AFFX-LysX-M_at 19.7 P 0.028457
AFFX-LysX-3_at 19.9 P 0.000127
AFFX-PheX-5_at 10.8 P 0.004998
AFFX-PheX-M_at 15.7 P 0.001593
AFFX-PheX-3_at 22.3 P 0.01667
AFFX-ThrX-5_at 14.6 P 0.00141
AFFX-ThrX-M_at 21.8 P 0.00039

Total number of rows: 15617

Table truncated, full table size 491 Kbytes.




Supplementary file Size Download File type/resource
GSM142316.CEL.gz 3.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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