|
| Status |
Public on Jun 01, 2011 |
| Title |
Control Individual 1 |
| 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: 1
|
| 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 |
C1
|
| 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 |
|
