GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM142320 Query DataSets for GSM142320
Status Public on Oct 25, 2007
Title MO control zebrafish embryo 21hpf-1
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
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 28 P 0.004484
AFFX-BioB-M_at 43.5 P 0.000169
AFFX-BioB-3_at 24.3 P 0.023929
AFFX-BioC-5_at 123.9 P 0.00006
AFFX-BioC-3_at 117.5 P 0.000052
AFFX-BioDn-5_at 238.3 P 0.000044
AFFX-BioDn-3_at 466.5 P 0.00007
AFFX-CreX-5_at 1426.5 P 0.000044
AFFX-CreX-3_at 2227.2 P 0.000044
AFFX-DapX-5_at 68.3 P 0.000095
AFFX-DapX-M_at 146 P 0.000258
AFFX-DapX-3_at 199.5 P 0.000044
AFFX-LysX-5_at 17 P 0.006187
AFFX-LysX-M_at 21.2 M 0.050229
AFFX-LysX-3_at 34.8 P 0.00011
AFFX-PheX-5_at 17.6 P 0.011384
AFFX-PheX-M_at 18.2 P 0.023929
AFFX-PheX-3_at 33.6 P 0.002023
AFFX-ThrX-5_at 22 P 0.004998
AFFX-ThrX-M_at 37.7 P 0.00039

Total number of rows: 15617

Table truncated, full table size 495 Kbytes.

Supplementary file Size Download File type/resource
GSM142320.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap