|
| Status |
Public on May 12, 2012 |
| Title |
Sn leaf_10_4_D/B_June1_Cy3 |
| Sample type |
RNA |
| |
|
| Source name |
leaf_9_1_C_Aug22
|
| Organism |
Sorghastrum nutans |
| Characteristics |
tissue: leaf
precipitation: varied
temperature: control
|
| Treatment protocol |
The RaMP facility can manipuate precipitation (ambient precipitation and altered precipitation) and temperature (ambient temperature and warming).
|
| Growth protocol |
Individuals of Andropogon gerardii and Sorghastrum nutans were sampled from the natural population in field from RaMP of Konza prairie in 2006
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions and purified with RNAeasy kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Genisphere kit (Array 900) Expression Array Detection kit
|
| |
|
| Hybridization protocol |
The labeled cDNA was hybridized overnight at 50C to cDNA microarrays, followed by a second hybridization of the dye molecules with the specific primers on the cDNAs. Advalytix SlideBooster hybridization station.
|
| Scan protocol |
Axon GenPix 4100 scanner at two wavelength, 652 and 532 nm, using GenePix software (V. 5) producing two-channel images.
|
| Description |
MSMI_13497104.gpr
Sample 92
|
| Data processing |
We loaded the GAL file for the SAM 1.2 maize microarray, aligned the spots using a template grid. Obvious anomalies in the grids were flagged as bad spots and then fluorescence intensity was assessed with GenePix. These results were queried for quality control. Features with signal to noise ratios less than ten were flagged bad and excluded from further analysis. The intersity values on each array were then normalized with the ratip of medians protocol according to the use manual. Prior to the high-throughput regression analysis, the fluorescence intensity were normalized by conducting mixed model ANOVAs with array and dye included as fixed effects: yij=X+Ai+Dj+(AXD)ij+Eij, where yij is the fluorescence intensity on the ith array and labeled with the jth dye, X is the mean, Ai is the effect of the ith array (i = 1-49 for Andropogon gerardii; i=1-50 for Sorghastrum nutans), Dj is the effect of the jth dye, (AXD)ij is the array-dye interaction and Eij is the stochastic error.
|
| |
|
| Submission date |
Feb 01, 2012 |
| Last update date |
May 12, 2012 |
| Contact name |
shenghua yuan |
| E-mail(s) |
shenghua.yuan@yale.edu
|
| Organization name |
Yale University
|
| Department |
Ecology and Evolutionary Biology
|
| Lab |
Smith
|
| Street address |
165 Prospect St.
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL4521 |
| Series (1) |
| GSE35492 |
The transcriptional profiles of bluestem and Indian grass - Konza 2006 [Zea mays; Andropogon gerardii; Sorghastrum nutans] |
|
