7 protocols
AccessionNameType
P-MTAB-26088
hybridization
Biotin-labeled cRNA samples were mixed in 300 mL of Hybridization Mix (Affymetrix; 900720) containing Hybridization Controls and Control Oligonucleotide B2 (Affymetrix; 900454). Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays and ATH1 arrays for 16 h at 45 C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol..
P-MTAB-26086
bioassay_data_transformation
Background correction, normalisation, and calculation of probe set summaries were done using RMA (Irizarry et al., 2003) implemented in the Aroma.Affymetrix package (Bengtsson et al., 2008).
P-MTAB-26087
bioassay_data_transformation
Data were log2-transformed by RMA.
P-MTAB-26089
image_acquisition
The arrays were scanned using an Affymetrix 3000 7G confocal scanner.
P-MTAB-26083
grow
Three successive experiments were carried out using seeds of the Arabidopsis thaliana accession Col-0 and osd1-1. For each experiment, seeds of about 20 siliques were harvested. Plants were grown under long-day conditions (16 h light and 8 h darkness) at 18 C.
P-MTAB-26085
labeling
RNA was amplified and labelled with the GeneChip® IVT Express Labelling kit (Affymetrix, Santa Clara, CA).
P-MTAB-26084
nucleic_acid_extraction
Seeds were harvested into 40 ul RNAlater (Sigma, Buchs, Switzerland) . Glass beads (1.25-1.55 mm) were added, and the samples were ground unfrozen in a Silamat S5 (Ivoclar Vivadent, Ellwangen, Germany). RNA was extracted using the RNAqueous kit (Ambion/Applied Biosystems, Lincoln, CA) combined with Plant RNA Isolation Aid (Ambion/Applied Biosystems) according to manufacturer’s instructions. The RNA was subjected to a DNase treatment.