|
| Status |
Public on Oct 30, 2008 |
| Title |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Root tip of 4 dpg seedling harvested immediated
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Genotype: Col-0
Root promeristem and cap
|
| Biomaterial provider |
Arabidopsis Stock Center
|
| Treatment protocol |
Seedlings at 4 dpg were transferred to a plate of 5% agar solid medium (1X MS salts, 0.5% sucrose) to ensure a hard support and the root tip was surgically excised under a dissecting microscope using a 30G sterile dental needle (ExelInt), with a cutting error of about 5 um. The plant was immediately returned to a standard 0.8% agar solid medium (1X MS salts, 0.5% sucrose) for recovery. For microarray analysis, 130 um of uncut tip or 70 um of regenerating stumps were manually excised with the 30G needle
|
| Growth protocol |
Plants were grown for 4 days in long day (16hr light/8hr dark) 22 oC conditions in a Percival (Percival Scientific). Plants were grown on agar in 1x MS All plant lines are in the Col-0 background.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sets of 5 tissue samples were collected each in 2.5 ul of extraction buffer (XB) of the Pico Pure RNA Isolation Kit (Araturus), flash-frozen in liquid nitrogen and ground. At least 25 samples were pooled for each experimental replicate (4 replicates)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA from all isolated samples was prepared according to the standard two-cycle Affymetrix protocol from 50 ng total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array in the Affymetrix Hybridization oven 640 following standard Affymetrix protocol. GeneChips were washed and stained using the 'EukGE-WS2v4_450' protocol in the Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to standard Affymetrix protocols.
|
| Description |
Roots grown horizontally on square plates
|
| Data processing |
The data was normlized using MAS5 with a target intensity of 250
|
| |
|
| Submission date |
Dec 20, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Kenneth David Birnbaum |
| E-mail(s) |
[email protected]
|
| Phone |
212-998-8257
|
| Organization name |
New York University
|
| Department |
Biology
|
| Lab |
Birnbaum
|
| Street address |
12 Waverly Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE9996 |
Organ regeneration in plants is independent of stem cell niche activity |
|
| Relations |
| Reanalyzed by |
GSE119083 |
