|
| Status |
Public on Mar 12, 2009 |
| Title |
Laser capture microdissected (LCM) seed coat at the mature green stage, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis mature green stage seed coat captured by LCM
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
development stage: mature green stage
tissue: seed coat captured by LCM
genotype: Ws-0
|
| Treatment protocol |
Siliques between 1.8-2.0 cm long containing mature green-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 |
Seed coat collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, 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 |
Mar 10, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
John J Harada |
| E-mail(s) |
jjharada@ucdavis.edu
|
| 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 |
| GSE15165 |
Expression data from Arabidopsis seed compartments at the mature green stage. |
|
| Relations |
| Reanalyzed by |
GSE119083 |
