|
| Status |
Public on Sep 02, 2010 |
| Title |
ear_6am_ day2 |
| Sample type |
RNA |
| |
|
| Source name |
ear_6am_rep1_ day2
|
| Organism |
Zea mays |
| Characteristics |
tissue: Immature Ear
cultivar: B73
developmental stage: 2-5mm
time: 6am day2
|
| Treatment protocol |
For Agilent microarray profiling, samples were taken starting at daybreak on day 1 (ZT0), and taken every 4 hours hence for 72 hours. At each time point, the top-most immature ear, 4-5 cm in length, was collected from two separate plants to create one of three biological field replicates.
|
| Growth protocol |
Plants of the public inbred line B73 were grown under field conditions in Johnston, Iowa, U.S.A. to V14-V15 stages, as defined according to the appearance of the leaf collar of the uppermost leaf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen ground tissue (SQ Tissue Kit, Omega Biotek), followed by polyA RNA isolation (Illustra mRNA Purification Kit, GE Biosciences) for the 108 samples. The total RNA and polyA RNA samples were visualized and quantified on Agilent’s Bioanalyzer to check for degradation and to determine the concentration.
|
| Label |
Cy3, Cy5
|
| Label protocol |
Each mRNA sample was made into double-stranded DNA, amplified by an in-vitro transcription reaction, and labeled with Cy3 or Cy5 fluorescent dye, all using Agilent’s Low RNA Linear Amp kit. Biological replicates were labeled alternately using Cy3 or Cy5 to guard against dye-bias.
|
| |
|
| Hybridization protocol |
Standard Agilent Hybridization protocol
|
| Scan protocol |
After hybridization, the microarray slides were washed and scanned immediately with Agilent’s G2505B DNA Microarray Scanner at two laser power settings (100% and 10%). The images were inspected visually for image artifacts, and feature intensities were extracted, filtered, and normalized with Agilent’s Feature Extraction Software (v 9.5.1).
|
| Description |
Gene Expression at ear_6am_rep1_ day2
|
| Data processing |
The data were then normalized using quantile normalization (BOLSTAD http://www.ncbi.nlm.nih.gov/pubmed/12538238) and passed forward for periodicity determination. Further quality control and downstream analysis were performed using data analysis tools in Rosetta’s Resolver Database and in the statistical program R
|
| |
|
| Submission date |
Sep 01, 2010 |
| Last update date |
Sep 01, 2010 |
| Contact name |
Kevin Robert Hayes |
| E-mail(s) |
[email protected]
|
| Organization name |
Pioneer Hi-Bred International
|
| Street address |
7200 NW 62nd Ave
|
| City |
Johnston |
| State/province |
IA |
| ZIP/Postal code |
50131-0184 |
| Country |
USA |
| |
|
| Platform ID |
GPL10837 |
| Series (2) |
| GSE23916 |
Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period |
| GSE23918 |
Diurnal Regulation of Gene Expression in Leaves and Immature Ears Over a 72-Hour Period |
|
