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Sample GSM823400 Query DataSets for GSM823400
Status Public on Oct 26, 2014
Title Brain Larvae salamander treatment: biological rep3
Sample type RNA
Source name Brains from tadpoles exposed by larvae salamander for 8days
Organism Rana pirica
Characteristics tissue: Brain
Treatment protocol Brain was dissected from each tadpole, and 10 brain tissues were collected together for one sample in a single tube containing RNAlater (QIAGEN RNA stabilization reagent) for subsequent use in producing RNA probes for the functional microarray analysis. The tissues were stored at -80°C until RNA extraction.
Growth protocol Tadpoles before growing hind rimb.
Extracted molecule total RNA
Extraction protocol Total RNA was obtained using the Qiagen RNA mini preparation system. RNA yield was measured by absorbance at 260 nm and the quality was assessed by confirming the integrity of the rRNA bands by electrophoresis.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Xenopus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using GeneChip Scanner 3000
Description Gene expression data from brain of Rana pirica tadpoles exposed by larval salamanders.
Data processing The data (SF:1.000; NF:1.000) were analyzed with summarization algorithm MAS 5 and using GeneSpringGX11.5.1. Baseline Transformation was set as median of Control Samples
Submission date Oct 27, 2011
Last update date Oct 26, 2014
Contact name Tsukasa Mori
Phone 01-(81)-466-84-3682
Fax 01-(81)-466-84-3682
URL http://01-(81)-466-84-3682
Organization name Nihon University
Department Bioresource Sciences
Lab Marine Molecular Biochemistry
Street address Kameino 1866
City Fujisawa
State/province Kanagawa
ZIP/Postal code 252−0880
Country Japan
Platform ID GPL1318
Series (1)
GSE33283 Gene expression data in the brain of tadpoles [Rana pirica] exposed by larvae salamander.

Data table header descriptions
VALUE MAS5 signal intensity

Data table
AFFX-BioB-5_at -0.05218506
AFFX-BioB-M_at 0.05388546
AFFX-BioB-3_at -0.429801
AFFX-BioC-5_at -0.33685207
AFFX-BioC-3_at -0.12276745
AFFX-BioDn-5_at -0.22447205
AFFX-BioDn-3_at -0.4458046
AFFX-CreX-5_at -0.4989891
AFFX-CreX-3_at -0.21738243
AFFX-DapX-5_at -0.8854332
AFFX-DapX-M_at -4.0289373
AFFX-DapX-3_at -1.0418539
AFFX-LysX-5_at -1.7043958
AFFX-LysX-M_at 0.1879549
AFFX-LysX-3_at -0.15011978
AFFX-PheX-5_at -1.7018609
AFFX-PheX-M_at -2.3182817
AFFX-PheX-3_at -1.7650266
AFFX-ThrX-5_at -1.5430045
AFFX-ThrX-M_at 0.4549675

Total number of rows: 15611

Table truncated, full table size 420 Kbytes.

Supplementary file Size Download File type/resource
GSM823400.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM823400.CHP.gz 90.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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