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Sample GSM142318 Query DataSets for GSM142318
Status Public on Oct 25, 2007
Title Spt5 knockdown zebrafish embryo 21hpf-1
Sample type RNA
 
Source name Spt5-targeted MO injected Danio rerio embryo, 21 hours post-fertilization
Organism Danio rerio
Characteristics strain: TL
age: 21 hours post-fertilization
The transcription factor Spt5 is knocked down.
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 Spt5-targeted morpholino oligo (5’-GTTTCTCTACAGTCTGTCGCTCCTG-3’) with a 3’ carboxyfluorescein (Gene Tools, LLC).
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 Spt5 knockdown 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 45.5 P 0.001248
AFFX-BioB-M_at 37.2 P 0.00011
AFFX-BioB-3_at 23.2 P 0.005565
AFFX-BioC-5_at 124.6 P 0.000044
AFFX-BioC-3_at 113.4 P 0.000052
AFFX-BioDn-5_at 259.7 P 0.000044
AFFX-BioDn-3_at 471.1 P 0.00007
AFFX-CreX-5_at 1680.9 P 0.000052
AFFX-CreX-3_at 2296.6 P 0.000044
AFFX-DapX-5_at 68.3 P 0.00007
AFFX-DapX-M_at 154.7 P 0.00039
AFFX-DapX-3_at 187.6 P 0.00006
AFFX-LysX-5_at 14.9 P 0.002867
AFFX-LysX-M_at 30.1 M 0.042962
AFFX-LysX-3_at 29 P 0.00007
AFFX-PheX-5_at 24 P 0.000258
AFFX-PheX-M_at 26.4 P 0.001796
AFFX-PheX-3_at 33.2 P 0.00039
AFFX-ThrX-5_at 30.8 P 0.004998
AFFX-ThrX-M_at 39.7 P 0.000258

Total number of rows: 15617

Table truncated, full table size 494 Kbytes.




Supplementary file Size Download File type/resource
GSM142318.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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