|
| Status |
Public on Aug 19, 2009 |
| Title |
wild type 1h FR repA |
| Sample type |
RNA |
| |
|
| Source name |
plant seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
growth stage: seedling
genotype: wild type
|
| Treatment protocol |
Approximately 100 seeds were plated on half MS and kept in the dark and cold for 3 days. Germination was induced by a 3 hours red light (50µmol/m2/s) and seedlings were kept in the dark for 3 days before being subjected to 1 or 24 hrs of 0.5 or 5µmol.m2.s1 of FR light.
|
| Growth protocol |
Seedlings were grown as described previously (Duek et al., 2004, Curr Biol, 14, 2296-2301). All mutants were in the Columbia background (Col) and the pif4pif5 double mutant has been described previously (Lorrain et al., 2008, Plant J, 53, 312-323).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seedlings were flash-frozen in liquid nitrogen, ground using a tissulyser (Qiagen) 2 times 30s, 30Hz without extraction buffer, then twice again in the presence of RLT extraction buffer (Qiagen). RNAs were extracted using the RNeasy plant mini kit (Qiagen) following the manufacturer’s recommendations except that 3 washes were done with the RLP buffer instead of 2.
|
| Label |
biotin
|
| Label protocol |
100ng of total RNA were amplified and labeled using the Message Amp II-biotin Enhanced reagents (Ambion; catalog #AM1791). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).
|
| |
|
| Hybridization protocol |
Arabidopsis ATH1 Genome Array (Affymetrix, Santa Clara, CA, USA) were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)
|
| Scan protocol |
Scanning was done on an Affymetrix GeneChip Scanner 7G
|
| Description |
Seedlings were kept in the dark for 3 days after germination before being subjected to 1 hr of 0.5µmol.m2.s1 of FR light
|
| Data processing |
Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).
|
| |
|
| Submission date |
May 28, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Sylvain Pradervand |
| E-mail(s) |
[email protected]
|
| Phone |
+41 21 692 39 08
|
| Organization name |
UNI Lausanne
|
| Department |
CIG
|
| Lab |
DNA Array Facility
|
| Street address |
Genopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE16333 |
Phytochrome Interacting Factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light. |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
