|
| Status |
Public on Oct 30, 2009 |
| Title |
SC2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
muscle, southern, control
|
| Organism |
Fundulus heteroclitus |
| Characteristics |
subspecies: heteroclitus
|
| Treatment protocol |
prior to heat shock 20ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen RNeasy mini kit following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Reverse transcriptase of 15ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen). Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).
|
| |
|
| Channel 2 |
| Source name |
muscle, pool
|
| Organism |
Fundulus heteroclitus |
| Characteristics |
type: Pooled RNA
subspecies: macrolepidotus and heteroclitus
|
| Treatment protocol |
at 20ºC or 60 min at 34ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen RNeasy mini kit following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Reverse transcriptase of 15ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen). Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).
|
| |
|
| |
| Hybridization protocol |
Hybridization followed the procedures at http://web.uvic.ca/grasp/microarray (Genisphere Array 50 Protocol).
|
| Scan protocol |
Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 65). Fluorescence intensity data were extracted from TIF images using Spotfinder (TIGR).
|
| Description |
none
|
| Data processing |
TM4 Microarray Software Suite, a set of open-source freeware programs developed at the Institute for Genomics Research (TIGR), was used for quantification, normalization and analysis of microarray data. The otsu quantification method within TIGR Spotfinder was used to quantify the scanned microarray files. Integrated intensities were corrected for background and any spots with expression levels < 2 standard deviations above background for at least 50% of the samples were removed. TIGR Microarray Data Analysis System (MIDAS) was used to apply a locally weighted linear regression (LOWESS) normalization module. The resulting normalized and filtered expression files were analyzed using TIGR Multiexperiment Viewer (MeV).
|
| |
|
| Submission date |
Oct 28, 2009 |
| Last update date |
Oct 29, 2009 |
| Contact name |
Wendy Tymchuk |
| E-mail(s) |
[email protected]
|
| Phone |
604-666-7909
|
| Fax |
604-666-3497
|
| Organization name |
Fisheries & Oceans Canada
|
| Department |
Science
|
| Lab |
CAER
|
| Street address |
4160 Marine Drive
|
| City |
West Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V7V1N6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2716 |
| Series (1) |
| GSE18792 |
The heat shock response of killifish (Fundulus heteroclitus): candidate gene and heterologous microarray approaches. |
|
