|
| Status |
Public on May 25, 2007 |
| Title |
Soybean_Cotyledon_ES2 |
| Sample type |
RNA |
| |
|
| Source name |
Soybean cotyledon-stage endosperm captured by LCM
|
| Organism |
Glycine max |
| Characteristics |
Laser capture microdissected (LCM) endosperm at the cotyledon stage, biological replicate 2
Soybean cv. Asgrow A3237
|
| Treatment protocol |
Seeds with length between 2.5 and 3.0 mm containing cotyledon-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al., Plant Physiol.132. 27-35 (2003)). Seed compartment was captured from eight-micron sections using a Leica LMD6000 system.
|
| Growth protocol |
Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).
|
| Label |
biotin
|
| Label protocol |
Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA). Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.
|
| |
|
| Hybridization protocol |
Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45°C with the GeneChip Soybean 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 |
Endosperm regions from cotyledon-stage seeds were microdissected using the LEICA LMD6000 system.
|
| Data processing |
The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.
|
| |
|
| Submission date |
May 23, 2007 |
| Last update date |
May 23, 2007 |
| Contact name |
Bob Goldberg |
| E-mail(s) |
[email protected]
|
| Phone |
310-825-3270
|
| Organization name |
University of California, Los Angeles
|
| Department |
Molecular, Cell and Developmental Biology
|
| Street address |
610 Charles E Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL4592 |
| Series (1) |
| GSE7881 |
Expression data from soybean seed compartments with embryos at the cotyledon stage |
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