|
| Status |
Public on Apr 26, 2015 |
| Title |
Leaf 3 hrs-1 |
| Sample type |
RNA |
| |
|
| Source name |
Leaf 3 hrs
|
| Organism |
Glycine max |
| Characteristics |
cultivar/genotype: William -82
age: 30 days
dehydated for: 3 hrs
tissue: leaves
|
| Treatment protocol |
After 30days, plants were subjected to water stress by removing them without touching th eplants. Leaves and Roots were harvested by flash freezing in liquid nitrogen. Nine plants were utlized for each time point( three replicates per time-point and three plants per replicate.)
|
| Growth protocol |
Soybean W-82 seeds were grown in hydrophonics using 0.5x Hoaglonad solution, ph5.8 in a growth chamber with a 16hrs/8hrs day/night cycle at 25°C and 50% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isloated for both tissues using Qiagen RNAeasy Midi Kit.
|
| Label |
Cy3
|
| Label protocol |
total RNA was amplified using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Ref. 11917-020). Amplified product was labeled using NimbleGen DNA Labeling Kit.
|
| |
|
| Hybridization protocol |
NimbleGen expression array hybridization using NimbleGen Hybridization Kit.
|
| Scan protocol |
NimbleGen MS-200 scanner with auto-gain - 2um scan
|
| Data processing |
NimbleScan v. 2.6
NimbleScan software normalizes expression data using quantile normalization as described by Bolstad, et al. (Bioinformatics 2003; 19:185). Gene calls are generated using the Robust Multichip Average (RMA) algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249). The *_532_norm_RMA.pair files do not have filtering. They have all 137,503 rows of probes (many of which are duplicates in this design). This corresponds to the number of records in the .ndf file. On the other hand, the *_532_RMA.calls files have 52,181 rows where duplicates have been combined (averaged).
|
| |
|
| Submission date |
Aug 05, 2013 |
| Last update date |
Apr 27, 2015 |
| Contact name |
Paul J Rushton |
| E-mail(s) |
paul.rushton@tamu.edu
|
| Phone |
(972) 952 9246
|
| Organization name |
Texas A&M AgriLife Research & Extension Center
|
| Street address |
17360 Coit Road
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75252 |
| Country |
USA |
| |
|
| Platform ID |
GPL17531 |
| Series (1) |
| GSE49537 |
Transcriptomics Analyses of soybean leaves and roots sample during water-deficit |
|
