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Sample GSM326286 Query DataSets for GSM326286
Status Public on Mar 31, 2009
Title Time 1, Experimental Replicate 1
Sample type RNA
 
Channel 1
Source name TEx1 (Time 1)
Organism Hippoglossus hippoglossus
Characteristics distal intestine
Day 1 of diet
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Triazole according to the manufacturers protocol
Label Cy5
Label protocol RNA (1 ug) from control RNA reference and experimental samples was reverse transcribed and labeled using the 3DNA Genisphere Array 900 expression array detection kit (Genisphere Inc,Hatfield PA, USA) with Alexa fluorophores according to manufacturers instructions.
 
Channel 2
Source name Univ RNA CEx
Organism Hippoglossus hippoglossus
Characteristics distal intestine
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Triazole according to the manufacturers protocol
Label Cy3
Label protocol RNA (1 ug) from control RNA reference and experimental samples was reverse transcribed and labeled using the 3DNA Genisphere Array 900 expression array detection kit (Genisphere Inc,Hatfield PA, USA) with Alexa fluorophores according to manufacturers instructions.
 
 
Hybridization protocol Hybridization was completed using the 3DNA kit from Genisphere, (60 uL) was carefully applied to one corner of the Lifter Slip on the slide and immediately placed in the hybridization chamber (Die Tech, San Jose, CA, USA) for ON hyb. The hybridization process is 2 step where the initial hyb is cDNA only, and the second hyb is to couple the fluorophore. After hybridization slides were washed.
Scan protocol Scanned on Perkin Elmer ScanArray 5000XL, ScanArray Express software v3.0.1
Description All experimental samples run against universal RNA (cDNA prepared from 1 ug of a pooled universal RNA consisting of equal amounts of RNA from five developmental stages from hatching until post-metamorphosis).
Data processing Limma LOWESS normalized, background subtracted data obtained from log2 of processed Experimental signal/processed Reference signal. Arraypipe software was used.
 
Submission date Oct 02, 2008
Last update date Dec 27, 2008
Contact name Jason Williams
E-mail(s) jason.williams@nrc-cnrc.gc.ca
Phone (902)426-5903
Fax (902)426-9413
Organization name National Research Council
Department Institute for Marine Biosciences
Lab Microarray
Street address 1411 Oxford Street
City Halifax
State/province Nova Scotia
ZIP/Postal code B3H 3Z1
Country Canada
 
Platform ID GPL6361
Series (1)
GSE13025 Halibut Soydiet Series

Data table header descriptions
ID_REF
VALUE log2 RATIO (Exp/Ref)
RATIO Ratio, based on the highest level intensity values available (normalized over background corrected over foreground intensities and merged over log-transformed over natural values). A value of 1 is equal to no change. Everything greater than 1 means a positive change (up-regulation) and everything smaller than 1 means a negative change (down-regulation) from one condition to another (usually from CH1 to CH2).

Data table
ID_REF VALUE RATIO
1
2 0.8206 1.76619
3
4
5 0.2822 1.21603
6
7 2.3742 5.18436
8
9
10
11 -1.7628 0.29468
12 -0.0255 0.98249
13 1.4761 2.78198
14
15
16 -0.6858 0.62164
17
18
19
20

Total number of rows: 9984

Table truncated, full table size 90 Kbytes.




Supplementary file Size Download File type/resource
GSM326286.gpr.gz 3.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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