|
| Status |
Public on Aug 21, 2017 |
| Title |
Ler D Imb (FR_Ler.2) |
| Sample type |
RNA |
| |
|
| Source name |
Imbibed seeds, wild-type Landsberg erecta, dormant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Landsberg erecta
genotype/variation: Wild-type
tissue: Whole seeds
plant stage: Dormant
protocol: Dormant seeds imbibed in water for 24h
|
| Treatment protocol |
RNA was extracted from whole seeds that were imbibed for 24h in water.
|
| Growth protocol |
For the transcriptome analyses of Ler and the NILs, plants were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from dry seeds using RNAqueous columns with Plant RNA isolation aid (Ambion) according to the manufacturer's protocol. The RNA was further purified through precipitations with isopropanol and a high-salt precipitation solution containing 0.24 M sodium citrate and 0.16 M sodium chloride and subsequently with 2 M lithium chloride. RNA was qualitatively assessed and quantified using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent) and NanoDrop1000 spectrometry (NanoDrop Technologies).
|
| Label |
biotin
|
| Label protocol |
RNA was processed and cRNA synthesized according to the 3' GeneChips OneCycle kit.
|
| |
|
| Hybridization protocol |
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 Affymetrix 3000G scanner.
|
| Description |
FR_Ler.2
|
| 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 (Ath1121501_At_TAIRG.cdf v18.0.0, released 23rd January 2014 obtained via http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/).
|
| |
|
| Submission date |
Nov 22, 2016 |
| Last update date |
Aug 22, 2017 |
| 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) |
| GSE90162 |
The identification of novel genes involved in seed dormancy and after-ripening in Arabidopsis thaliana |
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