|
| Status |
Public on Sep 30, 2009 |
| Title |
17_R |
| Sample type |
RNA |
| |
|
| Source name |
developing caryopsis from timepoint 28 and BiolRep2_DS
|
| Organism |
Triticum aestivum |
| Characteristics |
RNA Sample ID:11
TimePoint (DPA): 28
BiolRep:BiolRep2_DS
Array ID: 34
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from developing grains using TRIZOL (Invitrogen), treated with RQ1 DNAse (Promega) and was re-purified using RNA Easy columns (QIAGEN).
|
| Label |
Alexa 647
|
| Label protocol |
Ten microgram of total RNA was indirectly labeled with Alexa 555 and Alexa 647 fluorophores (Molecular Probes Inc) using the protocol recommended by the manufacturer.
|
| |
|
| Hybridization protocol |
Hybridization was carried out using the Pronto! Hybridization kit reagents (Corning Inc, NY) following the supplied protocol.
|
| Scan protocol |
Hybridized slides were scanned using a Genepix 4000B microarray scanner and raw spot fluorescence intensities were collected using GenePix Pro version 5.0.
|
| Description |
This study looked at 7835 genes in wheat caryopses.
|
| Data processing |
The logarithms (base 2) of the original intensity values, not the ratios, for each probe obtained from each fluorescent channel were used. To reduce any dye bias introduced during RNA labeling, the global median value of all the signals per channel on each individual array was subtracted from each spot raw intensity signal and divided by the standard deviation. The expression values per gene were centered based on the median value of expression of the gene across all time-points. We used SAS PROC STDIZE to normalize the data set by array and then by gene for all samples.
|
| |
|
| Submission date |
Sep 05, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Debbie Laudencia-Chingcuanco |
| Organization name |
USDA-ARS
|
| Department |
Western Regional Research Center
|
| Lab |
Genomics and Gene Discovery Research Unit
|
| Street address |
800 Buchanan Street
|
| City |
Albany |
| State/province |
CA |
| ZIP/Postal code |
94710 |
| Country |
USA |
| |
|
| Platform ID |
GPL5808 |
| Series (1) |
| GSE8963 |
Transcriptome profiling of wheat caryopsis development |
|
