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Sample GSM142319 Query DataSets for GSM142319
Status Public on Oct 25, 2007
Title Spt5 knockdown zebrafish embryo 21hpf-2
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 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 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
Phone +81-45-924-5798
Fax +81-45-924-5834
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
VALUE mean signal of the array feature
ABS_CALL mean detection of the array feature

Data table
AFFX-BioB-5_at 54.4 P 0.000754
AFFX-BioB-M_at 64.3 P 0.000052
AFFX-BioB-3_at 29.9 P 0.023929
AFFX-BioC-5_at 158.5 P 0.000044
AFFX-BioC-3_at 153 P 0.000052
AFFX-BioDn-5_at 361.6 P 0.000044
AFFX-BioDn-3_at 600.2 P 0.00006
AFFX-CreX-5_at 1852.2 P 0.000044
AFFX-CreX-3_at 2687.9 P 0.000044
AFFX-DapX-5_at 88.7 P 0.000095
AFFX-DapX-M_at 179.6 P 0.000446
AFFX-DapX-3_at 226.4 P 0.000044
AFFX-LysX-5_at 15.3 P 0.020022
AFFX-LysX-M_at 32.8 M 0.042962
AFFX-LysX-3_at 38 P 0.000446
AFFX-PheX-5_at 15.4 P 0.01667
AFFX-PheX-M_at 24.6 P 0.006871
AFFX-PheX-3_at 50.4 P 0.000509
AFFX-ThrX-5_at 22.5 P 0.004484
AFFX-ThrX-M_at 40.5 P 0.000509

Total number of rows: 15617

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM142319.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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