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Sample GSM142317 Query DataSets for GSM142317
Status Public on Oct 25, 2007
Title Untreated zebrafish embryo 21hpf-1
Sample type RNA
 
Source name 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 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 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 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 28.7 P 0.00141
AFFX-BioB-M_at 52.3 P 0.000095
AFFX-BioB-3_at 25.4 P 0.012547
AFFX-BioC-5_at 140.3 P 0.00007
AFFX-BioC-3_at 131.2 P 0.000044
AFFX-BioDn-5_at 271.2 P 0.000044
AFFX-BioDn-3_at 585.3 P 0.00006
AFFX-CreX-5_at 1864.7 P 0.000044
AFFX-CreX-3_at 3164.6 P 0.000044
AFFX-DapX-5_at 66.7 P 0.000095
AFFX-DapX-M_at 127.8 P 0.000754
AFFX-DapX-3_at 166.7 P 0.00007
AFFX-LysX-5_at 12.2 P 0.028457
AFFX-LysX-M_at 27 A 0.156732
AFFX-LysX-3_at 36.1 P 0.000258
AFFX-PheX-5_at 14.8 P 0.030976
AFFX-PheX-M_at 20.5 P 0.028457
AFFX-PheX-3_at 36.1 P 0.01667
AFFX-ThrX-5_at 33 P 0.026111
AFFX-ThrX-M_at 34.5 P 0.001796

Total number of rows: 15617

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM142317.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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