|
| Status |
Public on Jun 01, 2008 |
| Title |
cold - slideB - rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
cold seedling
|
| Organism |
Zea mays |
| Characteristics |
Strain: B73, Tissue: whole seedling, Age: 7 days
|
| Treatment protocol |
10ºC for 24 h, with the final 8 h in the dark
|
| Growth protocol |
planted 2 cm deep in 5 cm of sterilized vermiculite in plastic trays with bottom drainage holes to prevent water-logging. Trays were saturated with distilled, deionized water then placed under fluorescent illumination (16 h 350 uE m-2) on racks in a walk-in 26ºC room.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent (Invitrogen), purified by ethanol precipitation. Samples were concentrated using Qiagen (Valencia CA) MinElute columns
|
| Label |
Cy3
|
| Label protocol |
Total RNA (~1.5 ug) was labeled with either Cy3 or Cy5 using the Ambion Message Amp II target labeling kit (Ambion Cat # 1751) according to the manufacturers recommendations using reduced reaction reagents and volumes in order to conserve reagents. Complete details are available at http://www.maizearray.org/files/cRNA_Target_Production_Using_RNA_Amplification.pdf
|
| |
|
| Hybridization protocol |
Arrays were hybridized for 14 hours at 42 C in a hybridization buffer containing 50% formamide, 5X SSC, and 0.1% SDS. After hybridization, arrays were initially washed at 42 C in 2X SSC, 01% SDS for 5 minutes and then subject to two, five minute washes in 0.1X SSC at room temperature. Complete details are available at http://www.maizearray.org/files/Hybridization_Protocol_For_cRNA_Targets.pdf
|
| Scan protocol |
Arrays were scanned on an Axon 4100 AL scanner (Molecular Devices Corporation, Sunnyvale CA) at 95% laser power. Raw data was extracted from the resulting images using the GenePix 6.0 software. (Molecular Devices Corporation, Sunnyvale CA)
|
| Description |
total RNA extracted from pools of 10 siblings
|
| Data processing |
Each sample was hybridized 4 times to different other samples. The 2 dye intensities were imported into R and normalized with limma ( (lowess for within array, quantile for between arrays). Then the individual intensities were calculated and the 4 measurements for each sample were averaged..
|
| |
|
| Submission date |
Oct 29, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
John F Fernandes |
| E-mail(s) |
[email protected]
|
| Phone |
650-533-9376
|
| Organization name |
Stanford University
|
| Department |
Bio Sci
|
| Lab |
Walbot
|
| Street address |
385 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL1993 |
| Series (1) |
| GSE9453 |
Zea mays B73 stress treatments on UA 70mer oligo slides (Maize oligo array version 1.3 array A and B) |
|
