|
| Status |
Public on Jul 31, 2015 |
| Title |
4.CEL |
| Sample type |
RNA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: gi-100
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using RNeasy columns (Quiagen) and DNA removed with DNA-free reagents (Ambion) following manufacturer’s instructions. The quality of the isolated RNA was assessed with a Nanochip on the Bioanalyzer 2100 (Agilent).
|
| Label |
biotin
|
| Label protocol |
Total RNA samples (150 ng) were reverse transcribed into double-stranded cDNA and then in vitro transcribed in the presence of biotin-labeled nucleotides using the GeneChip 3′ IVT Express kit (Affymetrix; 901229) including poly(A) controls as recommended by the manufacturer. The quality and quantity of the biotinylated cRNA were determined using a NanoDrop ND 1000 and Bioanalyzer 2100.
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA samples (15 μg) were randomly fragmented for 35 min at 94°C in fragmentation buffer (Affymetrix). Biotinylated cRNA samples were mixed in 250 μL of Hybridization Mix (Affymetrix; 900720) containing Hybridization Controls and Control Oligonucleotide B2 (Affymetrix; 900454). Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.
|
| Scan protocol |
An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled targets.
|
| Description |
gi
|
| Data processing |
LOG2 RMA normalisation
|
| |
|
| Submission date |
Aug 01, 2014 |
| Last update date |
Jul 31, 2015 |
| Contact name |
Emiel Ver Loren van Themaat |
| E-mail(s) |
themaat@mpiz-koeln.mpg.de
|
| Organization name |
Max Planck Institute
|
| Street address |
Carl von linneweg
|
| City |
Cologne |
| ZIP/Postal code |
50823 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13479 |
| Series (1) |
| GSE59996 |
Identification of genes regulated by GIGANTEA (GI), the CYCLING DOF FACTORS (CDFs) and the GI-CDF module |
|
