Genetic properties of the MAGIC maize population
Experiment View
OverviewTest for MARS
Programme: Multi-modal plant project test
SEEK ID: https://datahub-test.elixir-belgium.org/projects/41
Public web page: Not specified
Organisms: No Organisms specified
Elixir Belgium PALs: No PALs for this Project
Project created: 11th Oct 2023
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Institutions: Default Institution, Vlaams Instituut voor Biotechnologie, uppsala University, ILVO
Data from Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays https://doi.org/10.1186/s13059-015-0716-z
Projects: Genetic properties of the MAGIC maize population
Web page: Not specified
WGS, RNAsequencing and genotyping of founders lines
Genome-seq_RNAseq_variants of founders lines
Submitter: Flora D'Anna
Investigation: Characterisation of founders lines
Assays: Genome Assembly, Genome Variants, Genome sequencing, Genomic, Genomic variants, Genomic variants, Library preparation, Library preparation, RNA extraction, RNA sequencing, Transcriptomics
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Genomic variants
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Submitter: Flora D'Anna
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Characterisation of founders lines
Study: Genome-seq_RNAseq_variants
Genome assembly protocol
Creator: Flora D'Anna
Submitter: Flora D'Anna
Library preparation was done using the TruSeq RNA Sample Preparation Kit v2 (Illumina). In brief, starting from total RNA the mRNA is purified using polyA selection. Following chemically fragmentation the mRNA is converted into single-stranded cDNA using random hexamer priming. Next, double-stranded cDNA is generated and adapters are ligated.
Creator: Flora D'Anna
Submitter: Flora D'Anna
Total RNA was extracted using TriZol.
Creator: Flora D'Anna
Submitter: Flora D'Anna
The basal 5 millimeter of the fourth leaf was sampled for RNA extraction harvested two days after its appearance from the surrounding older leaves.
Creator: Flora D'Anna
Submitter: Flora D'Anna
Plants were grown in the growth chamber under controlled growth conditions (24oC, 55% relative humidity, 170 mmol m-2 s-1 photosynthetically active radiation at plant level in a 16-h/8-h day/night cycle).
Creator: Flora D'Anna
Submitter: Flora D'Anna
Abstract (Expand)
Authors: M. Dell'Acqua, D. M. Gatti, G. Pea, F. Cattonaro, F. Coppens, G. Magris, A. L. Hlaing, H. H. Aung, H. Nelissen, J. Baute, E. Frascaroli, G. A. Churchill, D. Inze, M. Morgante, M. E. Pe
Date Published: 11th Sep 2015
Publication Type: Journal Article
Test for MARS
Input (Sample Name) (Registered Sample List) *, Analysis Title (String) *, Analysis Alias (String) *, Description (String) *, Experiment Type (Controlled Vocabulary - EVA Experiment Type CV) *, Reference (String) *, Raw Data File (String) *, File path (String) , Checksum type (String) , Checksum (String)
Not specified
Test for MARS
Input (FASTA) (Registered Sample List) *, Analysis Title (String) *, Analysis Alias (String) *, Description (String) *, Experiment Type (Controlled Vocabulary - EVA Experiment Type CV) *, Reference (String) *, Data file Name (String) *
Not specified
Genome assembly
Input (Raw Data File) (Registered Sample List) *, sequence assembly protocol (String) *, FASTA (String) *, FASTA URL (String) , ASSEMBLYNAME (String) *, ASSEMBLY_TYPE (Controlled Vocabulary - ENA ASSEMBLY_TYPE) *, COVERAGE (String) *, PROGRAM (String) *, PLATFORM (String) *, MOLECULETYPE (String)
Not specified
Input (library name) (Registered Sample List) *, nucleic acid sequencing (String) *, instrument_model (Controlled Vocabulary - sequencing instrument (free text allowed)) *, file type (Controlled Vocabulary - file type (free text allowed)) *, Raw Data File (String) *, MD5 (String)
Not specified
Genomic library preparation
Input (Sample Name) (Registered Sample List) *, library source (Controlled Vocabulary - library source (free text allowed)) *, library strategy (Controlled Vocabulary - library strategy (free text allowed)) *, library selection (Controlled Vocabulary - library selection (free text allowed)) *, library layout (Controlled Vocabulary - library layout (free text allowed)) *, library name (String) *, library construction (String) *
Not specified
Genome assembly
Input (Registered Sample List) *, sequence assembly protocol (String) *, FASTA (String) *, FASTA URL (String) , ASSEMBLYNAME (String) *, ASSEMBLY_TYPE (Controlled Vocabulary - ENA ASSEMBLY_TYPE) *, COVERAGE (String) *, PROGRAM (String) *, PLATFORM (String) *, MOLECULETYPE (String)
Test for MARS
Input (Registered Sample List) *, Analysis Title (String) *, Analysis Alias (String) *, Description (String) *, Experiment Type (Controlled Vocabulary - EVA Experiment Type CV) *, Reference (String) *, Data file Name (String) *
