https://researchdata.se/en/catalogue Search results en The data set contains Tiff Z-stacks from light-grown hypocotyls and cotyledons of cortical microtubule (CMT) reporter lines either with few or no ablated cells from a time series experiment. This data set was analyzed with a new semi-automated image analysis workflow we have developed to quantify CMTs reorganization in individual cells following an ablation (https://github.com/VergerLab/MT_Angle2Ablation_Workflow). The dataset in the zip file was analyzed using the scripts on GitHub (https://github.com/VergerLab/MT_Angle2Ablation_Workflow). A step by step describes and explains all the scripts of the image analysis procedure. The intermediate data generated by the analysis method can be found on zenodo (https://doi.org/10.5281/zenodo.7436075). The documentation file Example_2D_Image.tif gives a visual representation from a typical z-stack. Wed, 10 May 2023 10:49:17 GMT https://researchdata.se/en/catalogue/dataset/2022-252-1 https://researchdata.se/en/catalogue/dataset/2022-252-1 Swedish University of Agricultural Sciences Elsa Demes Stéphane Verger Confocal microscopy, electron microscopy and atomic force microscopy images of Arabidopsis thaliana roots, both in wild plants and mutant plants or plants under chemical treatment. The images show cell division phenotypes in pericycle cells, mainly stained with the specific cellulose dye calcofluor white. These results are part of an investigation that seeks to dissect the molecular bases that regulate the regeneration response in Arabidopsis roots after mechanical damage. Mechanical damage by herbivory or abiotic stress is common in nature in plants. Faced with this, plants have developed a rapid regeneration response that allows replacing damaged cells with new cells. In this study we demonstrate that the composition of the cell wall is important to optimize the regeneration response. Particularly, pectin plays a key role in cell-cell adhesion and cell proliferation after wounding. The microscopy images are provided as TIFF files along with metadata tables. The atomic force microscopy data also includes force maps created in JPK NanoWizard. Thu, 13 Feb 2025 15:02:19 GMT https://researchdata.se/en/catalogue/dataset/2024-612 https://researchdata.se/en/catalogue/dataset/2024-612 Swedish University of Agricultural Sciences Luciano Di Fino Peter Marhavy Supplementary information for manuscript: "Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq" from Lilit Nersisyan, Maria Ropat and Vicent Pelechano (2020) Dataset updated to fivepseq version1.0b6 5'P mRNA degradome datasets analyzed with fivepseq. (http://pelechanolab.com/software/fivepseq/). Raw Saccharomyces cerevisiae data is available from GEO under accession code GSE91064 and for Arabidopsis thaliana under accessions GSE72505 and GSE77549. Thu, 17 Sep 2020 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-12662153 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-12662153 Karolinska Institutet Vicent Pelechano Lilit Nersisyan Maria Ropat Phylogeny of LysM paralogs with sequences harvested from newly sequenced transcriptomes from Datisca glomerata and Ceanothus thyrsiflorus plus the following species as references: Arabidopsis thaliana, Cicer arietinum, Cucurbita pepo, Fragaria vesca, Glycine max, Lotus japonicus, Manihot esculenta, Medicago trunculata, Morus notabilis, Oryza sativa, Prunus persica, Ricinus communis, Solanum lycopersicum, Sorghum bicolor, Theobroma cacao, Vigna radiata and Ziziphus jujuba. Sequences were collected with blastp searches against the RefSeq database subset by the above list of species, using presumed D. glomerata and C. thyrsiflorus orthologs. Sequences were aligned with Clustal Omega (http://www.clustal.org/omega/; Sievers et al. 2014) and reliable alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM62 substitution matrix. Sequences that were identical after BMGE, were discarded. The tree was estimated with RAxML v. 8.2.4 (https://sco.h-its.org/exelixis/web/software/raxml/index.html; Stamatakis 2014) using the PROTGAMMAAUTO model and automatic bootstopping. Files provided are: 1. The full alignment after BMGE selection of positions and removal of identical sequences: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.phylip 2. The maximum likelihood tree labelled with bootstrap values in:a. newick format: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.besttree.newickb. Dendroscope (http://dendroscope.org/; Huson et al. 2007): lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.bipartitions.nexml Tue, 29 May 2018 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17045-sthlmuni-6384200 https://researchdata.se/en/catalogue/dataset/doi-10-17045-sthlmuni-6384200 Stockholm University Daniel Lundin Marco Guedes Salgado