|
Status |
Public on Jun 01, 2011 |
Title |
Control Individual 6 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Arctic charr gill tissue whole RNA reverse transcribed to cDNA, control
|
Organism |
Salvelinus alpinus |
Characteristics |
tissue: gill condition: before temperature stress group: control individual: 6
|
Treatment protocol |
200 Arctic charr were exposed to heat stress. 10 fish were sampled before the stress (control). Six randomly sampled fish in this group were used for microarray analysis.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from gill tissues disrupted and homogenized in 1 ml TRIzol reagent using a Mixer-mill (Retch® MM 301) with tungsten carbide beads. Phase separation was conducted using 200 µl chloroform, and RNA was purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
|
Label |
Cy5
|
Label protocol |
cDNA (300 ng) and aRNA (500 ng) were labeled with Cy5 and Cy3 (Amersham Biosciences), respectively, using Invitrogen’s SuperScript Indirect cDNA Labeling System following the manufacturer's instructions.
|
|
|
Channel 2 |
Source name |
reference aRNA
|
Organism |
Salmo salar |
Characteristics |
tissue: gonad, brain, spleen
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from gill tissues disrupted and homogenized in 1 ml TRIzol reagent using a Mixer-mill (Retch® MM 301) with tungsten carbide beads. Phase separation was conducted using 200 µl chloroform, and RNA was purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
|
Label |
Cy3
|
Label protocol |
cDNA (300 ng) and aRNA (500 ng) were labeled with Cy5 and Cy3 (Amersham Biosciences), respectively, using Invitrogen’s SuperScript Indirect cDNA Labeling System following the manufacturer's instructions.
|
|
|
|
Hybridization protocol |
Details of the microarray hybridization process can be found at the University of Victoria cGRASP website (http://web.uvic.ca/grasp/microarray/array.html) within the .pdf document entitled Invitrogen Indirect cDNA Labeling System version 3.
|
Scan protocol |
Images were scanned on a ScanArray™ Express Microarray Scanner (Packard BioScience BioChip Technologies, model #ASCEX00). Slides were scanned at 74 and 72 PMT for Cy3 and Cy5, respectively, and spot intensity was calculated with ImaGene ver. 6.5.1.
|
Description |
C6
|
Data processing |
All statistical analyses of the microarray data were conducted using Genespring ver. 7.3.1. Signals were normalized per spot and per chip using an intensity-dependent (LOWESS) normalization, then per gene to normalize to the median. Spots were filtered on flags present, and only spots with signals greater or equal to the average base/proportional value of the raw channel were retained.
|
|
|
Submission date |
Dec 27, 2010 |
Last update date |
Jun 01, 2011 |
Contact name |
Nicole Lisa Quinn |
E-mail(s) |
nicole_quinn@sfu.ca
|
Organization name |
Simon Fraser University
|
Department |
Molecular Biology and Biochemistry
|
Lab |
Davidson, SSB 6150
|
Street address |
8888 University Drive
|
City |
Burnaby |
State/province |
BC |
ZIP/Postal code |
V5A 1S6 |
Country |
Canada |
|
|
Platform ID |
GPL10096 |
Series (2) |
GSE26306 |
Arctic charr exposed to acute thermal stress |
GSE29610 |
Identification of genes expressed during and following exposure to chronic moderate temperature stress in Arctic charr |
|