tissue: Abscission zone regions of siliques position 4 to 8 genotype: IDA T-DNA knockout ecotype: Col-0
Growth protocol
Fill in the details, example: Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers Vötsch VB 1514 (Vötch Industrietechnik GmbH, Germany) with a 16/8 h (light/dark) photoperiod at 22/18 °C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity.
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated with the Spectrum Plant Total RNA Kit (Sigma, St. Louis,MO,USA) and was quantified with NanodropND 1000 (Nanodrop Technologies, Wilmington, DE, USA).
Label
Cy5
Label protocol
Total RNA (15 mg) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction. Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.
Channel 2
Source name
Abscission zone regions of siliques position 4 to 8, control (biological replica 3)
tissue: Abscission zone regions of siliques position 4 to 8 genotype: wild type ecotype: Col-0
Growth protocol
Fill in the details, example: Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers Vötsch VB 1514 (Vötch Industrietechnik GmbH, Germany) with a 16/8 h (light/dark) photoperiod at 22/18 °C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity.
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated with the Spectrum Plant Total RNA Kit (Sigma, St. Louis,MO,USA) and was quantified with NanodropND 1000 (Nanodrop Technologies, Wilmington, DE, USA).
Label
Cy3
Label protocol
Total RNA (15 mg) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction. Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.
Hybridization protocol
Hybridizations were performed in a Slide Booster Hybridization Station (Advalytix, Brunnthal, Germany), and the slides were washed according to the manufacturers’ descriptions (Genisphere and Advalytix).
Scan protocol
The slides were scanned at 10 mm resolution on a G2505B Agilent DNA microarray scanner (Agilent Technologies,Palo Alto, CA, USA). The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).
Description
Two color microarray. Biological replicas are dye-swaped between slides.
Data processing
Spots identified as not found or which were manually flagged out as bad were filtered out. The data sets were log-transformed and normalized using the printtip-loess approach. Within-array replicated measurements for the same gene were merged by taking the average between the replicates. The data were then scaled so that all array data sets had the same median absolute deviation. No background normalization was done. The differentially expressed genes were identified using the Limma software package. References: Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3 (2004)
INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and its receptors HAE/HSL2 are required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana (part 2)
INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and its receptors HAE/HSL2 are required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana
Data table header descriptions
ID_REF
VALUE
normalized log2 ratio representing IDA T-ko plants / wild type control plants
