DOI: 10.5061/dryad.pnvx0k6wp
title: Data from: Multiscale chromatin dynamics and high entropy in plant iPSC ancestors

description: Plant protoplasts provide a starting material to induce pluripotent cell
 masses in vitro competent for tissue regeneration. Dedifferentiation is
 associated with large-scale chromatin reorganisation and massive
 transcriptome reprogramming, characterized by stochastic gene expression.
 How this cellular variability reflects on chromatin organisation in
 individual cells and what are the factors influencing chromatin
 transitions during culturing is largely unknown. High-throughput imaging
 and a custom, supervised image analysis protocol extracting over 100
 chromatin features unravelled a rapid, multiscale dynamics of chromatin
 patterns which trajectory strongly depends on nutrients availability.
 Decreased abundance in H1 (linker histones) is hallmark of chromatin
 transitions. We measured a high heterogeneity of chromatin patterns
 indicating an intrinsic entropy as hallmark of the initial cultures. We
 further measured an entropy decline over time, and an antagonistic
 influence by external and intrinsic factors, such as phytohormones and
 epigenetic modifiers, respectively. Collectively, our study benchmarks an
 approach to understand the variability and evolution of chromatin patterns
 underlying plant cell reprogramming in vitro.
description: Image features extracted by Tissue Maps from microscopy images
 following automated, supervised segmentation of plant protoplast
 nuclei.  Leaf protoplasts  were cultured in
 coverglass-bottom 96-well plates and imaged using a confocal microscope
 Cell Voyager. The plant cell line (expressing  specific nuclear
 reporters), imaging day (day0-day7) and culturing media is indicated in
 the dataset. Additional information is provided in the Table S3 in the
 manuscript. Image features correspond to three
 families: intensity, morphology and texture. A complete list of image
 features used for the study is available as Table S2 in the
 manuscript.
description: # Multiscale chromatin dynamics and high entropy in plant iPSC ancestors
 [https://doi.org/10.5061/dryad.pnvx0k6wp](https://doi.org/10.5061/dryad.pnvx0k6wp) The HTI datasets correspond to image features extracted from high-throughput imaging of Arabidopsis leaf protoplasts cultures (multi-well plate) expressing fluorescent chromatin markers and cultivated several days under distinct media. The experiments description of the culturing medium, specific treatment, the imaging day, replicate culture number and marker line is provided in Table S4 of the related paper and associated with this link. The image features were extracted by TissueMaps ([http://tissuemaps.org](http://tissuemaps.org) following segmentation of the cell's nuclei labelled with H2B-RFP (See the related paper). The features are derived from a package described by Hamilton et al (2007). The data provide for each segmented nuclei: morphology descriptors of the segmented nuclei, signal intensity variables for each marker (H1.2-GFP and H2B-RFP), and texture features. There are four families of texture features (LBP, TAS, Gabor and Hu). Textures metrics describe the spatial distribution of signal intensities as a function of scale (Depeursinge et al., 2017a; Di Cataldo & Ficarra, 2017). The images used for segmentation are available at [IDR or DRYAD link to the images, in preparation] **Description of the dataset structure** * Mapobject_id : unique identifier of segmented nucleus * Day: Culturing day at imaging * Treatment: compound added to the culturing medium (eg, TSA, phytohormones) * Medium: culturing medium (Gamborg or W5, see Table S3 of related paper) * Line: Plant line used to prepare the protoplast culture (see Table S4 of related paper) * Well: well number on the multi-well plate used for plant cells cultures and imaging (see Methods in related paper) * Columns with prefix Morphology_: morphological descriptors of the object (nucleus). * Columns with prefix Intensity_: signal intensity descriptors (sum, mean, standard deviation) for each channel (C01= channel 1, H1.2-GFP ; C02= channel 2, H2B-RFP). In addition, Intensity_Mean_Ratio is the ratio of Intensity_Mean_C01/ Intensity_Mean_C02 * Columns with prefix Texture_: texture descriptors for 4 families of texture (LBP, Gabor, TAS and Hu, see Table S1 and main text of related paper) # Software These data were exported from TissueMaps after segmentation. [http://docs.tissuemaps.org/latest/](http://docs.tissuemaps.org/latest/) **References** Depeursinge, A., Fageot, J., & Al-Kadi, O. S. (2017b). Fundamentals of Texture Processing for Biomedical Image Analysis. 1-27. doi:10.1016/b978-0-12-812133-7.00001-6 Di Cataldo, S., & Ficarra, E. (2017). Mining textural knowledge in biological images: Applications, methods and trends. *Comput Struct Biotechnol J, 15*, 56-67. doi:10.1016/j.csbj.2016.11.002 Hamilton, N. A., Pantelic, R. S., Hanson, K., & Teasdale, R. D. (2007). Fast automated cell phenotype image classification. *BMC Bioinformatics, 8*, 110. doi:10.1186/1471-2105-8-110