|
| Status |
Public on Apr 25, 2008 |
| Title |
Arabidopsis GEP6 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis globular stage embryo proper captured by LCM
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Genotype: Ws-0
|
| Treatment protocol |
Siliques with length between 1.1 and 1.4 cm containing globular stage seeds were collected from 38-46 day old plants. Seeds were either dissected out of siliques or left in sub-divided siliques and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on 5 or 7 um sections using a Leica LMD6000 system. Compartments were only captured from seeds with globular embryos 24-32 um in diameter, as determined by a medial section through the embryo proper.
|
| Growth protocol |
Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.
|
| Label |
biotin
|
| Label protocol |
2 to 4 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.
|
| |
|
| Hybridization protocol |
Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G System.
|
| Description |
Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 2
Embryo proper collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.
|
| Data processing |
The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.
|
| |
|
| Submission date |
Apr 25, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
John J Harada |
| E-mail(s) |
[email protected]
|
| Phone |
530-752-0673
|
| Organization name |
University of California, Davis
|
| Department |
Plant Biology
|
| Lab |
Harada
|
| Street address |
One Shields Avenue
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE11262 |
Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage. |
| GSE12404 |
Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development |
|
| Relations |
| Reanalyzed by |
GSE119083 |
