|
| Status |
Public on Aug 07, 2015 |
| Title |
5%DMSO/0.1%Tween 20 in H20 - 2 |
| Sample type |
RNA |
| |
|
| Source name |
Emergent but non-fully-expanded 4th leaf_Dimethyl sulfoxide/Tween 20/H2O
|
| Organism |
Zea mays |
| Characteristics |
cultivar: Golden Queen
tissue: Leaf
|
| Treatment protocol |
For gene expression analysis, spot application of 10-OPEA was carried out by applying four 10µl droplets of either the control solution [ (H20/DMSO/0.1% Tween 20) (95:5:0.1; v/v/v)] or the same containing 2mM 10-OPEA onto the middle portion of partially emerged leaf 4 of 14-day old plants approximately 15 cm from the distal tip with 2 droplets on each side of the midrib 2 cm apart. At 90 min post treatment, control and 10-OPEA treated tissues were collected in liquid N2.
|
| Growth protocol |
Zea mays (variety Golden Queen) seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Nucleospin RNA Plant kit (Macherey-Nagel bmbH Inc., Duren, Germany) according to the manufacturers protocol and First Strand cDNA was synthesized using the Superscript III First Strand cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) with random decamer primers.
|
| Label |
biotin
|
| Label protocol |
For each sample, 1 μg of total RNA was provided to the University of Florida Interdisciplinary Center Biotechnology Research (UF-ICBR) Gene Expression Core for cDNA synthesis, reverse transcription, and biotin labeling using the Affymetrix GeneChip 3′ IVT express kit and protocol (Affymetrix).
|
| |
|
| Hybridization protocol |
Biotin labeled samples were hybridized to Affymetrix maize GeneChips at UF-ICBR using a GeneChip Hybridization Oven 640 with standard hybridization protocol
|
| Scan protocol |
Affymetrix maize GeneChips were scanned at UF ICBR with a GeneChip Scanner 3000 7G per standard procedure
|
| Description |
Dimethyl sulfoxide/Tween 20/H2O
|
| Data processing |
Data extraction was executed by the UF ICBR gene expression core and provided as CEL files. Data analysis was performed using ArrayStar 4 software (DNASTAR, Inc.). To minimize probe-specific affinity differences, all data were preprocessed using Robust MultiArray Analysis and quantile normalization.
|
| |
|
| Submission date |
Jun 08, 2015 |
| Last update date |
Aug 07, 2015 |
| Contact name |
Alisa Huffaker |
| E-mail(s) |
ahuffaker@ucsd.edu
|
| Phone |
858-534-3988
|
| Organization name |
UC San Diego
|
| Department |
Cell & Developmental Biology
|
| Street address |
9500 Gilman Drive #0116
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0116 |
| Country |
USA |
| |
|
| Platform ID |
GPL4032 |
| Series (1) |
| GSE69659 |
Maize death acids, 9-lipoxygenase derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators |
|
