|
| Status |
Public on Jul 16, 2013 |
| Title |
Seed_COT_3h_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Excised Cotyledons, 3h after sowing
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
accession: Columbia-0 (Col-0, N60000)
tissue: Embryo
seed part: COT
time: 3h
|
| Treatment protocol |
At eleven stages after sowing seeds were dissected into four parts (as detailed above) using a stereo microscoop, pair of pincers and a scalpel knife.
|
| Growth protocol |
Seeds of Arabidopsis accession Columbia-0 (Col-0, N60000) were sown on 0.7% water agarose (Eurogentec) and incubated in a germination cabinet at 22°C with continuous light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction a Stratagene kit was used (Agilent Technologies, Absolutely RNA Nanoprep kit, 50 preps, cat# 400753).
|
| Label |
biotin
|
| Label protocol |
The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. For each sample 100 ng was used as input.
|
| |
|
| Hybridization protocol |
Fragmented cRNA at a final concentration of 0.0375ng/μl was used for hybridization. The GeneChip (#900720) HWS Kit was used for hybridization, washing and staining.
|
| Scan protocol |
The scanning was performed using the Affymetrix 3000G scanner
|
| Description |
COT3.2
Sample redone for QC reasons
|
| Data processing |
The data was analysed using RMA in the affy Bioconductor package in R, using the v14.0.0 Arabidopsis CustomCDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF
|
| |
|
| Submission date |
Sep 28, 2012 |
| Last update date |
Jul 16, 2013 |
| Contact name |
Simon Peter Pearce |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nottingham
|
| Department |
Plant and Crop Sciences
|
| Street address |
Sutton Bonington Campus
|
| City |
Sutton Bonington |
| State/province |
Leicestershire |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16112 |
| Series (1) |
| GSE41212 |
Arabidopsis thaliana seed germination timecourse |
|
