|
| Status |
Public on Feb 22, 2008 |
| Title |
B84 11-day seedling aerial tissue; bio rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
Zea mays 11-day seedling aerial tissue genotype B84
|
| Organism |
Zea mays |
| Characteristics |
Genotype: B84; Stage: 11-day old seedling, all aerial tissue
|
| Growth protocol |
Seeds for maize inbreds and hybrids were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression analysis. Three biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 30ºC and night temperature of 22ºC) and sampled between 8:00 and 9:00 am. The plants were cut immediately above the highest brace root, thus all above-ground tissues and meristems were collected. Each biological replicate consisted of pooled tissue from eight different seedlings of the same genotype. The sampled tissues were flash frozen in liquid nitrogen and stored at -80 C prior to RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were isolated using TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy system (QIAGEN, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
Hybridization target was prepared according to an RNA amplification protocol posted at http://www.maizearray.org/maize_protocols.shtml
|
| |
|
| Hybridization protocol |
The 70-mer arrays were hybridized on a Tecan 4800 HS Pro hybridization station (Tecan Services Inc., Durham, NC) which is capable of processing 12 arrays in a single hybridization run.
|
| Scan protocol |
The arrays were scanned on an Axon 4100 AL scanner (Molecular Devices Corporation, Sunnyvale, CA) immediately after being hybridized.
|
| Description |
B84 11-day seedling aerial tissue versus pooled reference; bio rep 1
|
| Data processing |
Per chip and per gene normalizations using GeneSpring version 7.2; Cy3 normalized as a single channel; multiple normalizations based on different comparisons and analyses. Cy5 reference channel data was used for filtering out bad spots (ratio data was not generated).
|
| |
|
| Submission date |
Feb 15, 2008 |
| Last update date |
Feb 21, 2008 |
| Contact name |
Robert M Stupar |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota
|
| Department |
Agronomy and Plant Genetics
|
| Street address |
1991 Upper Buford Circle
|
| City |
Saint Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL6438 |
| Series (2) |
| GSE10542 |
Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis - 70mer |
| GSE10543 |
Gene expression variation among eight maize inbreds - 70mer oligo array |
|
