|
| Status |
Public on Dec 22, 2011 |
| Title |
bio4-1 mutant, watered with 200µM biotin, leaves, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
bio4-1 mutant, watered with 200µM biotin, leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: leaves
genotype/variation: bio4-1 mutant
age: 5 week old plants
|
| Treatment protocol |
After transfer to soil plants were watered once a week either with 1L water for a tray containing 28 pot with 1 plant each or with 1L 200µM d-biotin. Samples were collected from rosette leaves of five week old plants and each sample was pooled from 5 individuals.
|
| Growth protocol |
The seeds were stored at +4ºC, and were kept in the dark in water at +4ºC for 2 days before move to growth room. Seeds were then germinated on MS/2 (Sigma-Aldrich, St. Louis, MO) plates and one-week-old seedlings transferred to soil (1:1 peat: vermiculite; Finnpeat B2, Kekkilä Oyj, Tuusula, Finland). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of 50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen's RNeasy Plant mini kit's protocol according to the instructions of the manufacturer with additional precipitation step for the final eluate (1/10 vol 3 M NaAc pH 5.2 and 1 vol isopropanol added, incubation at -20 C for 2 h, centrifuge 13000 rpm 30 min, wash with 70% EtOH, drying, resuspension in DEPC treated MQ water. RNA integrity was checked with Agilent Bioanalyzer 2100 using Agilent RNA 6000 Pico Gene chips.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared using Affymetrix Enzo Kit from 3 ug total RNA and performed at the NASC's International Affymetrix Service
|
| |
|
| Hybridization protocol |
Hybridisation was performed according to the Affymetrix GeneChip Technical Analysis Manual at the NASC's International Affymetrix Service
|
| Scan protocol |
GeneChips were scanned using the Agilent 2500A GeneArray Scanner at the NASC's International Affymetrix Service
|
| Description |
bio4-1 mutant, watered once a week with 200µM biotin, 1l per tray with 28 plants, leaves were harvested and pooled from five plants , rep2
|
| Data processing |
The data were analyzed with the R-package using AffylmGUI; Robust multiarray average (RMA) normalization has been performed.
|
| |
|
| Submission date |
Jan 14, 2011 |
| Last update date |
Dec 23, 2011 |
| Contact name |
Günter Brader |
| E-mail(s) |
guenter.brader@ait.ac.at
|
| Organization name |
Austrian Institute of Technology
|
| Department |
Health & Environment Department
|
| Street address |
AIT
|
| City |
Seibersdorf |
| ZIP/Postal code |
2444 |
| Country |
Austria |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE26631 |
Effect of biotin deficiency on gene expression in Aravbidopsis leaves |
|
