|
| Status |
Public on Apr 27, 2007 |
| Title |
Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 2 (SRB) |
| Sample type |
RNA |
| |
|
| Source name |
SRB globular stage suspensor captured by LCM
|
| Organism |
Phaseolus coccineus |
| Characteristics |
SRB cv. Hammond's Dwarf Red Flowers
|
| Treatment protocol |
Flowers were hand-pollinated and tagged. Six days after pollination, seeds containing globular-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)). Embryo region was captured from six-micron sections using a Leica AS LMD System.
|
| Growth protocol |
SRB cv. Hammond's Dwarf Red Flower 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 |
Approximately 137 ng of total RNA was amplified using the MessageAmp II Kit (Ambion, Austin, TX) and SMART III primer (Clontech). Approximately 200 ng of cDNA derived from the amplified RNA was used for biotinylated cRNA synthesis using the ENZO BioArray High Yield RNA Transcript Labeling Kit.
|
| |
|
| Hybridization protocol |
Following fragmentation, nine 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 |
Suspensor regions from globular embryos were microdissected using the LEICA AS LMD 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 |
Apr 24, 2007 |
| Last update date |
Apr 24, 2007 |
| Contact name |
Bob Goldberg |
| E-mail(s) |
bobglab@mcdb.ucla.edu
|
| 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) |
| GSE7592 |
Expression data from SRB embryo regions at the globular stage |
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