Multiscale chromatin dynamics and high entropy in plant iPSC ancestors

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..., 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., , # 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 mark...