{"identifier":"map-by-seq_CLSM-stacks","title":"Rapid Identification of a Natural Knockout Allele of ARMADILLO REPEAT-CONTAINING KINESIN1 That Causes Root Hair Branching by Mapping-By-Sequencing - CLSM z-stack part on ARK1 cytoskeletal localisation and treatment in leaf epidermal cells","description":"This is the CLSM experimental part of a study which identified ARK1 with a mapping-by-sequencing approach to be causative for a root hair branching phenotype in one Arabidopsis thaliana accession of an accession panel. It is intended to serve as a microscopic use cases and initial example ARC for further development and conversion steps of ARCs with other microscopy-related studies and structures. In the overarching study, we developed a strategy for Arabidopsis thaliana studies using different natural accessions to identify causative genes for distinct phenotypes in which an interesting phenotype is found which is only represented by one or a few accessions. While the method of mapping-by-sequencing was developed already earlier, this study focusses on complementing GWAS studies for theses specific cases of low statistical power for causal gene detection in order to identify also genes underlying phenotypes of interest to a study with a low minor allele frequency in the panel.","submissionDate":"2014-05-31","publicReleaseDate":"2014-09-23","ontologySourceReferences":[{"description":"Experimental Factor Ontology","file":"http://www.ebi.ac.uk/efo/efo.owl","name":"EFO","version":"3.49.0"},{"description":"Scholarly Contributions and Roles Ontology","file":"http://purl.org/spar/scoro","name":"SCORO","version":"1.9.1"}],"publications":[{"pubMedID":"25248719","doi":"10.1104/pp.114.244046","authorList":"Louai Rishmawi; Hequan Sun; Korbinian Schneeberger; Martin Hülskamp; Andrea Schrader","title":"Rapid identification of a natural knockout allele of ARMADILLO REPEAT-CONTAINING KINESIN1 that causes root hair branching by mapping-by-sequencing","status":{"annotationValue":"published","termSource":"EFO","termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796"}}],"people":[{"lastName":"Schrader","firstName":"Andrea","email":"andrea.schrader@uni-koeln.de","address":"50674 Cologne, Germany","affiliation":"Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne","roles":[{"annotationValue":"contact person","termSource":"SCORO","termAccession":"http://purl.org/spar/scoro/contact-person"},{"annotationValue":" data-curator","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/data-curator"},{"annotationValue":" leads investigation","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/leads-investigation"},{"annotationValue":" designs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/designs-experiments"},{"annotationValue":" supervisor","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/supervisor"},{"annotationValue":" performs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/performs-experiments"},{"annotationValue":" analyses data","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/analyses-data"}],"comments":[{"name":"Investigation Person ORCID","value":"0000-0002-3879-7057"}]},{"lastName":"Huelskamp","firstName":"Martin","email":"martin.huelskamp@uni-koeln.de","address":"50674 Cologne, Germany","affiliation":"Institute for Plant Sciences - Molecular Cell Biology and Developmental Genetics & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne","roles":[{"annotationValue":"contact person","termSource":"SCORO","termAccession":"http://purl.org/spar/scoro/contact-person"},{"annotationValue":" principal investigator","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/principal-investigator"},{"annotationValue":" leads investigation","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/leads-investigation"},{"annotationValue":" designs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/designs-experiments"},{"annotationValue":" supervisor","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/supervisor"}],"comments":[{"name":"Investigation Person ORCID","value":"0000-0003-4165-6754"}]}],"studies":[{"filename":"ARK1-cytoskeletal-localisation/isa.study.xlsx","identifier":"ARK1-cytoskeletal-localisation","title":"localisation of YFP-ARK1 constructs in leaf epidermal cells in presence and absence of microtubules or actin.","description":"Constructs expressing YFP-tagged ARK1 used in the mapping-by-sequencing study are analyzed by live cell fluorescence CLSM. Oryzalin treatment disrupts microtubules which impairs observed YFP-ARK1 localisation while DMSO control treatment does not show this effect. Latrunculin B treatment disrupts actin as controlled by lifeact-eGFP. The cytoskeletal localisation suggest a mechanism how ARK1 affects branching of root hairs as observed in the accession underlying the mapping of the study and supports the causality of a mutation in ARK1 in the respective accession for its root hair branching phenotype. Maximum projections (2D stacks of maximal pixel intensity) of representative fluorescence CLSM z-stacks are included in the respective publication.","submissionDate":"2014-05-31","publicReleaseDate":"2014-09-23","publications":[{"pubMedID":"25248719","doi":"10.1104/pp.114.244046","authorList":"Louai Rishmawi; Hequan Sun; Korbinian Schneeberger; Martin Hülskamp; Andrea Schrader","title":"Rapid identification of a natural knockout allele of ARMADILLO REPEAT-CONTAINING KINESIN1 that causes root hair branching by mapping-by-sequencing","status":{"annotationValue":"published","termSource":"http://www.ebi.ac.uk/efo/EFO_0001796","termAccession":"EFO"}}],"people":[{"lastName":"Schrader","firstName":"Andrea","email":"andrea.schrader@uni-koeln.de","address":"50674 Cologne, Germany","affiliation":"Data Science and Management","roles":[{"annotationValue":"contact person","termSource":"SCORO","termAccession":"http://purl.org/spar/scoro/contact-person"},{"annotationValue":" data-curator","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/data-curator"},{"annotationValue":" leads investigation","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/leads-investigation"},{"annotationValue":" designs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/designs-experiments"},{"annotationValue":" performs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/performs-experiments"},{"annotationValue":" analyses data","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/analyses-data"}],"comments":[{"name":"Investigation Person ORCID","value":"0000-0002-3879-7057"},{"name":"Worksheet"}]},{"lastName":"Huelskamp","firstName":"Martin","email":"martin.huelskamp@uni-koeln.de","address":"50674 Cologne, Germany","affiliation":"Institute for Plant Sciences - Molecular Cell Biology and Developmental Genetics & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne","roles":[{"annotationValue":"contact person","termSource":"SCORO","termAccession":"http://purl.org/spar/scoro/contact-person"},{"annotationValue":" principal investigator","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/principal-investigator"},{"annotationValue":" leads investigation","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/leads-investigation"},{"annotationValue":" designs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/designs-experiments"}],"comments":[{"name":"Investigation Person ORCID","value":"0000-0003-4165-6754"},{"name":"Worksheet"}]},{"lastName":"Schrader","firstName":"Andrea","email":"andrea.schrader@uni-koeln.de","address":"50674 Cologne, Germany","affiliation":"Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne","roles":[{"annotationValue":"designs experiments","termSource":"SCORO","termAccession":"http://purl.org/spar/scoro/designs-experiments"},{"annotationValue":" performs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/performs-experiments"},{"annotationValue":" analyses data","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/analyses-data"}],"comments":[{"name":"Investigation Person ORCID"},{"name":"Worksheet","value":"0000-0002-3879-7057"}]},{"lastName":"Schrader","firstName":"Andrea","email":"andrea.schrader@uni-koeln.de","address":"50674 Cologne, Germany","affiliation":"Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne","roles":[{"annotationValue":"designs experiments","termSource":"SCORO","termAccession":"http://purl.org/spar/scoro/designs-experiments"},{"annotationValue":" performs experiments","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/performs-experiments"},{"annotationValue":" analyses data","termSource":" SCORO","termAccession":" http://purl.org/spar/scoro/analyses-data"}],"comments":[{"name":"Worksheet","value":"0000-0002-3879-7057"}]}],"studyDesignDescriptors":[{"annotationValue":"in vivo design; Controlled Before-After Studies","termSource":"http://purl.obolibrary.org/obo/OBI_0001199; http://purl.obolibrary.org/obo/OMIT_0028626","termAccession":"OBI; OMIT"}],"assays":[{"filename":"CLSM-stacks_oryzalin/isa.assay.xlsx","measurementType":{"annotationValue":"protein localization","termSource":"http://purl.obolibrary.org/obo/GO_0008104","termAccession":"GO"},"technologyType":{"annotationValue":"Confocal Microscopy","termSource":"http://purl.obolibrary.org/obo/NCIT_C17753","termAccession":"NCIT"},"technologyPlatform":"TCS-SPE confocal microscope DM5500Q (Leica Microsystems); LCS Lite 2.05 software (Leica Microsystems)"},{"filename":"CLSM-stacks_latrunculinB/isa.assay.xlsx","measurementType":{"annotationValue":"protein localization","termSource":"http://purl.obolibrary.org/obo/GO_0008104","termAccession":"GO"},"technologyType":{"annotationValue":"Confocal Microscopy","termSource":"http://purl.obolibrary.org/obo/NCIT_C17753","termAccession":"NCIT"},"technologyPlatform":"TCS-SPE confocal microscope DM5500Q (Leica Microsystems); LCS Lite 2.05 software (Leica Microsystems)"},{"filename":"CLSM-stacks_DMSO/isa.assay.xlsx","measurementType":{"annotationValue":"protein localization","termSource":"http://purl.obolibrary.org/obo/GO_0008104","termAccession":"GO"},"technologyType":{"annotationValue":"Confocal Microscopy","termSource":"http://purl.obolibrary.org/obo/NCIT_C17753","termAccession":"NCIT"},"technologyPlatform":"TCS-SPE confocal microscope DM5500Q (Leica Microsystems); LCS Lite 2.05 software (Leica Microsystems)"},{"filename":"YFP-ARK1_running-person-icon/isa.assay.xlsx","measurementType":{"annotationValue":"protein localization","termSource":"http://purl.obolibrary.org/obo/GO_0008104","termAccession":"GO"},"technologyType":{"annotationValue":"Confocal Microscopy","termSource":"http://purl.obolibrary.org/obo/NCIT_C17753","termAccession":"NCIT"},"technologyPlatform":"TCS-SPE confocal microscope DM5500Q (Leica Microsystems); LCS Lite 2.05 software (Leica Microsystems)"}],"factors":[{"factorName":"oryzalin treatment; latrunculinB treatment; DMSO treatment","factorType":{"annotationValue":"chemical treatment; chemical treatment; chemical treatment","termSource":"http://purl.obolibrary.org/obo/EO_0007189; http://purl.obolibrary.org/obo/EO_0007189; http://purl.obolibrary.org/obo/EO_0007189","termAccession":"EFO; EFO; EFO"}}]}]}
