|
| Status |
Public on Oct 01, 2009 |
| Title |
rosette_leaves_fdh_biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
fdh mutant (allele = fdh-3940; 2-bp insertion in exon-1 from FDH gene;Yephremov A. and al., The Plant Cell 11:2187-2202 (1999)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Young rosette leaves 2mm to 1cm
|
| Treatment protocol |
The samples were harvested in the morning; each sample was harvested on a liquid nitrogen/ice bath and then deep-frozen in liquid nitrogen. Each sample contained tissue from 15 typical plants. A harvest round comprised a WT, a bdg, a fdh and a lcr sample; three rounds of harvesting were made sequentially. When all samples were gathered, they were transferred to a -80°C freezer until extraction.
|
| Growth protocol |
Plants were grown on soil for 5,5 weeks and a half, under Short day 8 h day/ 16h night; 20°C/18°C into a growth chamber
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the RNeasy Plant Mini Kit (QIAGEN) + DNase1 (QIAGEN) according to the manufacturer instructions. At the end, total RNA was eluted into 80 µl of RNase free water. Quality and concentration were evaluated on a 1,5% agarose gel by loading 0,5µl of each sample. Sample were kept frozen at -80°C until shipment.
|
| Label |
biotin
|
| Label protocol |
cRNA were prepared by in vitro translation and labelled with biotin starting from 5µg of total RNA and according to the Affymetrix Manual (Expression Analysis Technical Manual; P/N 702232 Rev. 2/ 2005-2006)
|
| |
|
| Hybridization protocol |
After cleaning and fragmentation, 15µg of biotinylated cRNA were hybridized on ATH1 Genome Arrays (Affymetrix, 900385). GeneChips were then washed and stained on a Fluidics Station 450 (protocol: EukGE-WS2v4; Expression Analysis Technical Manual; P/N 702232 Rev. 2/ 2005-2006).
|
| Scan protocol |
Microarrays were then scanned using a GeneChip Scanner 3000.
|
| Description |
Gene expression data from young fdh rosette leaves
|
| Data processing |
The data were preprocessed using the Bioconductor packages affy and GC-RMA (fullmodel; with default settings).
|
| |
|
| Submission date |
Mar 04, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Derry Voisin |
| E-mail(s) |
[email protected]
|
| URL |
http://www.mpiz-koeln.mpg.de/english/research/saedlerGroup/yephremov/index.html
|
| Organization name |
Max Planck Institute for Breeding Research
|
| Department |
Saedler
|
| Lab |
Yephremov
|
| Street address |
Carl-von-Linne weg 10
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE15105 |
Probing gene misregulation in bodyguard, lacerata and fiddlehead mutants |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
