Comment[ArrayExpressAccession]	E-MTAB-1061
Investigation Title	Molecular profiling of Arabidopsis triploid maternal excess seeds
Comment[Submitted Name]	Molecular profiling of Arabidopsis triploid maternal excess seeds
Experiment Description	Transcriptome changes  in seeds derived from crosses of osd1 (omission of second division 1) maternal plants pollinated with wild-type pollen in comparison to wild-type plants pollinated with wild-type pollen at 6DAP. Seeds of about 20 siliques were manually isolated and used to extract RNA. Plants were grown under long day conditions at 18 C.
Experimental Design	individual_genetic_characteristics_design	in_vivo_design	co-expression_design	all_pairs
Comment[AEExperimentType]	transcription profiling by tiling array
Experimental Factor Name	Genotype
Experimental Factor Type	genotype
Quality Control Type	biological_replicate
Public Release Date	2012-12-12
Person Last Name	Hennig
Person First Name	Lars
Person Email	lars.hennig@slu.se
Person Phone	++46 18 67 3326
Person Address	Department of Plant Biology and Forest Genetics, Uppsala BioCenter, PO-Box 7080, SE-75007 Uppsala, Sweden
Person Affiliation	Swedish University of Agricultural Sciences and Linnean Center for Plant Biology
Person Roles	submitter
Protocol Name	P-MTAB-26083	P-MTAB-26084	P-MTAB-26085	P-MTAB-26086	P-MTAB-26087	P-MTAB-26088	P-MTAB-26089
Protocol Type	grow	nucleic_acid_extraction	labeling	bioassay_data_transformation	bioassay_data_transformation	hybridization	image_acquisition
Protocol Description	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.	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 manufacturerM-^Rs instructions. The RNA was subjected to a DNase treatment. 	RNA was amplified and labelled with the GeneChipM-. IVT Express Labelling kit (Affymetrix, Santa Clara, CA).	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). 	Data were log2-transformed by RMA.	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..	The arrays were scanned using an Affymetrix 3000 7G confocal scanner.
SDRF File	E-MTAB-1061.sdrf.txt
PubMed ID	23326241
Publication Author List	Kradolfer D, Hennig L, KM-CM-6hler C.
Publication Title	Increased maternal genome dosage bypasses the requirement of the FIS polycomb repressive complex 2 in Arabidopsis seed development.
Publication DOI	10.1371/journal.pgen.1003163