{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["stephanie huguet"],"study_type":["transcription profiling by array"],"organism":["Zea mays"],"species":["Zea mays"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-22948"],"description":["affy_diversity_maize - affy_diversity_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of two maize lines Cm484 (line of good digestibility) and F98902 (line of bad digestibility) at the same developmental stage (male flowering).  Keywords: organ comparison 4 arrays - maize"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Processing - no treatment","Nucleic Acid Extraction - cm484pl_2:342.3ng.","Growth Protocol - stem - - Greenhouse conditions: - hygrometry 77% night and 63% day - temperature 20°C night and 22°C day - Light 10h night and 14h day","Nucleic Acid Extraction - cm484pl_1:416.8ng.","Nucleic Acid Extraction - f98pl_2:120.7ng.","Labeling - labelling Biotin direct, amplification=yes, cRNA 20 ug.","Nucleic Acid Extraction - Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.","Hybridization - labelled extract quantity: 10ug","Nucleic Acid Extraction - f98pl_1:312.4ng.","Growth Protocol - stem - Greenhouse conditions: - hygrometry 77% night and 63% day - temperature 20°C night and 22°C day - Light 10h night and 14h day"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Magalie Pichon","stephanie huguet","Sandrine Balzergue","Stephanie Huguet","Marie-Laure Martin-Magniette"],"data_protocol":["Feature Extraction - The data were normalized with the gcrma algorithm (Irizarry et al., 2003) using R-2.6.2 version and AFFYMETRIX Bioconductor packages (Gentleman and Carey, 2002).","Assay Data Transformation - ID_REF = ID number<br>VALUE = GCRMA normalized signal intensity","Image Adquisition - GCOS, Biotin:pmt voltage 570nm,650V,laser power 1"],"additional_accession":[]},"is_claimable":false,"name":"affy_diversity_maize-Understanding the Diversity of Maize Cell Wall","description":"affy_diversity_maize - affy_diversity_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of two maize lines Cm484 (line of good digestibility) and F98902 (line of bad digestibility) at the same developmental stage (male flowering).  Keywords: organ comparison 4 arrays - maize","dates":{"release":"2011-07-14T00:00:00Z","modification":"2023-08-11T07:05:19.588Z","creation":"2022-03-07T03:11:22.393Z"},"accession":"E-GEOD-22948","cross_references":{"GEO":["GSE22948"],"EFO":["EFO_0002768"]}}