|
| Status |
Public on May 21, 2009 |
| Title |
flower_round_repl 2 |
| Sample type |
RNA |
| |
|
| Source name |
anthesis flowers
|
| Organism |
Solanum pimpinellifolium |
| Characteristics |
genotype: round-fruited LA1589 NIL
phenotype: round fruit
developmental stage: Anthesis stage
|
| Growth protocol |
Tomato LA1589 sun NILs were grown under standard conditions with supplemental lighting in the greenhouse in OARDC/the Ohio State University, Wooster, Ohio
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from 10-day preanthesis flower buds, anthesis flowers and fruits at 5 dpa of the LA1589 sun NILs that differ at sun using Trizol reagent (Invitrogen Inc. USA). Before RNA extraction, tissues harvested at 7-day interval from five plants were pooled for each genotype.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
none
|
| Data processing |
Background correction and data normalization were performed on raw data extracted by NimbleGen Systems Inc.by Robust Microarray Analysis (RMA) in Bioconductor. Differentially expressed genes (DEs) among the three stages were selected by multiple testing package multtest of R (www.r-project.org) using the RMA expression values.
|
| |
|
| Submission date |
Mar 30, 2009 |
| Last update date |
May 21, 2009 |
| Contact name |
Esther van der Knaap |
| E-mail(s) |
vanderknaap.1@osu.edu
|
| Phone |
330 263 2821
|
| Fax |
330 263 3887
|
| URL |
http://www.oardc.ohio-state.edu/vanderknaap/
|
| Organization name |
The Ohio State University
|
| Department |
Horticulture and crop science
|
| Lab |
Van der Knaap Laboratory
|
| Street address |
1680 Madison Ave.
|
| City |
Wooster |
| State/province |
OH |
| ZIP/Postal code |
44691 |
| Country |
USA |
| |
|
| Platform ID |
GPL8362 |
| Series (1) |
| GSE15453 |
Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape |
|
