|
| Status |
Public on Jan 27, 2010 |
| Title |
Arabidopsis bCZE2-2 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis bending cotyledon stage chalazal endosperm captured by LCM
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genome/variation: Ws-0
cell type: chalazal endosperm
developmental stage: bending cotyledon stage
|
| Treatment protocol |
Siliques containing bending cotyledon stage seeds were collected from 38-46 day old plants. Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on sections using a Leica LMD6000 system.
|
| 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 |
5 to 6 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) chalazal endosperm at the bending cotyledon stage, biological replicate 2
Chalazal endosperm collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined 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 |
Jan 26, 2010 |
| Last update date |
Jan 26, 2010 |
| 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) |
| GSE12404 |
Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development |
| GSE20039 |
Expression data from Arabidopsis seed compartments at the bending coyledon stage |
|
