|
| Status |
Public on Sep 21, 2014 |
| Title |
hda9_dryseed_ Biological replicate_3 |
| Sample type |
RNA |
| |
|
| Source name |
hda9_dryseed
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: hda9-1 mutant
tissue: dry seeds
|
| Treatment protocol |
Dry seeds were used obtained from 18-19 day-old (days after polination) ripe siliques
|
| Growth protocol |
Plants were grown on soil containing a mixture of substrate and vermiculite (3:1) in growth cabinets (Elbanton BV, Kerkdriel, The Netherlands) in 16h light at 22oC and 8h dark at 16oC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Ambion protocol from 1 ug total RNA (MessageAmp II-Biotin Enhanced Kit, 2008, Ambion)
|
| |
|
| Hybridization protocol |
After fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained with Fluidics Script FS450_004 in the Affymetrix Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G
|
| Description |
Gene expression data from dry hda9-1 mutant seeds, replicate 3
|
| Data processing |
The RMA algorithm implemented in R package AFFY was used for background correction, normalization and expression calculation. Statistical analysis of the normalized data were performed using R packages LIMMA and RankProd
|
| |
|
| Submission date |
Sep 11, 2013 |
| Last update date |
Sep 21, 2014 |
| Contact name |
Yong Li |
| E-mail(s) |
yong.li@uniklinik-freiburg.de
|
| Organization name |
Medical Center - University of Freiburg
|
| Department |
Institute of Genetic Epidemiology
|
| Street address |
Hugstetter Str. 49
|
| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE50786 |
Comparison of histone deacetylase 9-1 mutant (SALK_001723) dry seed transcriptome with Col wild-type |
|
