|
| Status |
Public on Aug 24, 2016 |
| Title |
CVI, AR imbibed (AR_RAD3.3) |
| Sample type |
RNA |
| |
|
| Source name |
After-ripened seeds imbibed in water for 3h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: CVI
plant stage: After-ripened seeds
protocol: After-ripened seeds imbibed in water
time: 3h
tissue: seed
tissue compartment: RAD (radicle and hypocotyl)
|
| Treatment protocol |
CVI samples: RNA was extracted from whole dry seeds and dissected seeds that were imbibed for 3, 7, 12 and 24 hours in water.
|
| Growth protocol |
For the transcriptome analysis of CVI, plants were grown in three replicates on rockwool supplemented with a standard nutrient solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CVI samples: RNA of the RAD samples was isolated with the Absolutely RNA Nanoprep kit (Agilent Technologies), RNA of the MCE and dry seed samples was isolated by an alternative method based on the hot borate isolation protocol and additionally cleaned up with NucleoSpin RNA Clean-Up XS (Macherey-Nagel).
|
| Label |
biotin
|
| Label protocol |
CVI: RNA was processed and cRNA synthesized by use of the 3’ IVT-Express Labeling Kit (#901229).
|
| |
|
| Hybridization protocol |
CVI samples: The GeneChip (#900720) HWS kit was used for hybridisation, washing and staining of the cartridges.
|
| Scan protocol |
Scanning of the arrays was performed using the Affimetrix 3000G scanner.
|
| Description |
AR_RAD3.3
CVI, dissected seed
|
| Data processing |
The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm using a custom chip definition file (.cdf) from the CustomCDF project [66] (Ath1121501_At_TAIRG.cdf v18.0.0, released 23rd January 2014 obtained via http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/).
|
| |
|
| Submission date |
Jan 15, 2016 |
| Last update date |
Aug 24, 2016 |
| Contact name |
Leónie Bentsink |
| E-mail(s) |
[email protected]
|
| Phone |
+31317481325
|
| Organization name |
Wageningen University
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708 PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21063 |
| Series (1) |
| GSE76907 |
Dormant and after-ripened seeds are distinguished by early transcriptional differences in the imbibed state |
|
