|
| Status |
Public on Dec 18, 2015 |
| Title |
6H, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
6 hours imbibed seeds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Col-0
plant organ: seeds
developmental stage: 6 hours imbibed seeds
|
| Treatment protocol |
Three thousand seeds at each developmental stage were selected using a stereomicoscope.
|
| Growth protocol |
Seeds were cold stratified for 72 h at 4˚C in 9 cm Petri dishes on two layers of blue filter paper and 10 ml of distilled water. After stratification, seeds were transferred to germination cabinets with constant white light at 22 ˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted following the hot borate protocol modified from Wan and Wilkins (1994) (Maia et al, Plos ONE 2011)
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cDNA was prepared using the Affymetrix NuGEN Ovation PicoSL WTA and Biotin Module from 50ng total RNA according to the manufacturer's specifications.
|
| |
|
| Hybridization protocol |
Following fragmentation, 2.5 ug of ss-cDNA were hybridized on the Affymetrix ARAGene 1.1ST Array plates. Plates were washed and stained by the GeneTitan machine using the Affymetrix HWS Kit for the GeneTitan.
|
| Scan protocol |
Plates were scanned using the Affymetrix GeneTitan scanner operated by the software program Affymetrix GeneChip Command Console.
|
| Description |
Gene expression data from Arabidopsis seeds imbibed for 6 hours
|
| Data processing |
The Robust Multichip Analysis (RMA-Sketch for gene level analysis) algorithm was used for the summarization. Signal intensities were extracted and analysed using the Bioconductor packages of R. The data was normalized using the RMA algorithm with the TAIRG v17 cdf file.
|
| |
|
| Submission date |
Jan 28, 2015 |
| Last update date |
Dec 18, 2015 |
| Contact name |
Anderson Tadeu Silva |
| Organization name |
Wageningen University
|
| Department |
Plant Physiology
|
| Lab |
Seed Lab
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| State/province |
Gelderland |
| ZIP/Postal code |
6708PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19371 |
| Series (1) |
| GSE65394 |
Time-series of the seed-to-seedling transition in Arabidopsis thaliana |
|
