|
| Status |
Public on Oct 02, 2014 |
| Title |
FSW 1hr #1_FW-->SW+As 1hr #3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
FSW 1hr #1
|
| Organism |
Fundulus heteroclitus |
| Characteristics |
tissue: gills
exposure type: Freshwater to seawater for 1 hour
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNAeasy kits were used for RNA extraction (Qiagen, Valencia, CA). Tissue samples were homogenized on ice with guanidine isothyocyanate with a Tissue-Tearor (Biospec Products, Barlesville, OK), with RNA being preciptated with equal parts ethanol. After washing and elution with nuclease free water on a glass fiber column, samples were treated with DNase
|
| Label |
Cy3
|
| Label protocol |
ds cDNA was labeled with NimbleGen Dual Color Labeling Kit per manufacturers recommendations to produce enough labeled product for a 12 x 135k microarray chip.
|
| |
|
| Channel 2 |
| Source name |
FW-->SW+As 1hr #3
|
| Organism |
Fundulus heteroclitus |
| Characteristics |
tissue: gills
exposure type: Freshwater to seawater for 1 hour with arsenic
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNAeasy kits were used for RNA extraction (Qiagen, Valencia, CA). Tissue samples were homogenized on ice with guanidine isothyocyanate with a Tissue-Tearor (Biospec Products, Barlesville, OK), with RNA being preciptated with equal parts ethanol. After washing and elution with nuclease free water on a glass fiber column, samples were treated with DNase
|
| Label |
Cy5
|
| Label protocol |
ds cDNA was labeled with NimbleGen Dual Color Labeling Kit per manufacturers recommendations to produce enough labeled product for a 12 x 135k microarray chip.
|
| |
|
| |
| Hybridization protocol |
Hybridizations were conducted in a Roche multi-chambered hybridization unit. Hybridization and post hybridization washing were performed using Hybridization Kit and Wash Buffer Kit per manufacturers recommendations (Roche Nimblegen). Hybridization reactions for subarrays 1 through 6 were loaded with displacement pipette, with overflow being removed. Hybrization commenced at 42°C for 17 hours, then washed with four SSC and SDS was buffers, then dried at 2000 x g for 1 minute.
|
| Scan protocol |
Arrays were scanned using Axon GenePix 4200A Professional Scanner
|
| Description |
gill
|
| Data processing |
Quantile normalization was perfomed on all samples. Following normalization, the Log2 (Cy3/Cy5) ratio of intensities was computed for each dual hybridization.
|
| |
|
| Submission date |
May 16, 2013 |
| Last update date |
Oct 02, 2014 |
| Contact name |
Richard Nathan Keith |
| E-mail(s) |
[email protected]
|
| Organization name |
Indiana University
|
| Department |
School of Public and Environmental Affairs
|
| Lab |
Joseph Shaw
|
| Street address |
1315 R. 10th St.
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL14994 |
| Series (1) |
| GSE47035 |
Genes enabling phenotypic plasticity evolve canalized gene expression by their limited associations with transcriptional regulators |
|
