3 protocols
AccessionNameType
P-MTAB-29530
bioassay_data_transformation
The probe intensity level background was removed using robust multichip analysis (RMA, (reference 1 below)). Probe intensity levels were then quantile normalised (reference 2 below). Array groups corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only (reference 1 below), by performing a per-probe set two-way analysis of variance(ANOVA, with factors 'probe' and 'stage'). This results in average expression levels over the biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. reference 1: Irizarry, R.A., B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, and T.P. Speed. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264. reference 2: Bolstad, B.M., R.A. Irizarry, M. Astrand, and T.P. Speed. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
P-MTAB-29529
bioassay_data_transformation
The probe intensity level background was removed using robust multichip analysis (RMA, (reference 1 below)). Probe intensity levels were then quantile normalised (reference 2 below). Array groups corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only (reference 1 below), by performing a per-probe set two-way analysis of variance(ANOVA, with factors 'probe' and 'stage'). This results in average expression levels over the biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. reference 1: Irizarry, R.A., B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, and T.P. Speed. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264. reference 2: Bolstad, B.M., R.A. Irizarry, M. Astrand, and T.P. Speed. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
P-MTAB-29528
nucleic_acid_extraction
RNA was isolated using RNeasy columns (Qiagen, Hilden, Germany) according to the manufacturers protocol. A first cycle of amplification was performed according to the GeneChip Eukaryotic small sample target labeling assay version II (affymetrix). After this a second round of amplification was performed as described in labelling protocol. (Parameters: Extracted product = total_RNA, Amplification = RNA polymerases)