DOI: 10.5061/dryad.8gtht770q
title: Cell-sheet shape transformation by internally-driven, oriented forces

description: During morphogenesis, cells collectively execute directional forces that
 drive the programmed folding and growth of the layers, forming tissues and
 organs. The ability to recapitulate aspects of these processes in vitro
 will constitute a significant leap forward in the field of tissue
 engineering. Free-standing, self-organizing, cell-laden matrices are
 fabricated using a sequential deposition approach that uses liquid
 crystal-templated hydrogel fibers to direct cell arrangements. The
 orientation of hydrogel fibers is controlled using flow or boundary cues,
 while their microstructures are controlled by depletion interaction and
 probed by scattering and microscopy. These fibers effectively direct cells
 embedded in a collagen matrix, creating multilayer structures through
 contact guidance and by leveraging steric interactions amongst the cells.
 In uniformly aligned cell matrices, oriented cells exert traction forces
 that can induce preferential contraction of the matrix. Simultaneously,
 the matrix densifies and develops anisotropy through cell remodeling. Such
 an approach can be extended to create cell arrangements with arbitrary
 in-plane patterns, allowing for coordinated cell forces and
 pre-programmed, macroscopic shape changes. This work reveals a
 fundamentally new path for controlled force generation, emphasizing the
 role of a carefully designed initial orientational field for manipulating
 shape transformations of reconstituted matrices.
description: # Cell-Sheet Shape Transformation by Internally-Driven, Oriented Forces
 Dataset DOI: [10.5061/dryad.8gtht770q](10.5061/dryad.8gtht770q) ##
 Description of the data and file structure Title of Dataset: Cell-Sheet
 Shape Transformation by Internally-Driven, Oriented Forces This dataset
 contains the data presented in the main text figures and supplemental
 information of "Cell-Sheet Shape Transformation by Internally-Driven,
 Oriented Forces", by authors Junrou Huang, Juan Chen, and Yimin Luo
 in Advanced Material. (Journal citation: J. Huang, J. Chen, Y. Luo, Adv.
 Mater., 2025, 2416624.
 [http://doi.org/10.1002/adma.202416624](http://doi.org/10.1002/adma.202416624)). Descriptions of the data and file structure: Data are all provided in comma separated value form (CSV). File names refer to the figures numbers of the manuscript. Processing scripts and image analyzed are also uploaded. If the letter S is provided before the number, the figure can be found in the Supporting Information. **Main text** Fig. 1a-1c contain schematics, no quantitative data presented. Figure 1a. Graphic representation of different ways to fabricate anisotropic structures. Figure 1b-c. Characterization of anisotropic and isotropic structure. Figure 1d. Wide angle and small angle X-ray scattering of the order and disordered PEG fibers. The data can be found as a csv, where q denotes the wave vector. Intensity represents the cumulative scattering intensity, which are used to generated the scattering plot. Type denotes the alignment of the substrate, which are either isotropic or nematic. The scattering intensity is obtained either by wide-angle X-ray scattering (WAXS) or small angle X-ray scattering (SAXS). The data set csv file is in folder "Figure 1". Figure 1e. Schematics depicting the postulated microscopic picture based on the scattering data. Fig. 2a-2c contain image data, no quantitative data presented. Figure 2a. Schematic depicting the fabrication of aligned cell assemblies. Figure 2b-c. Microscopy image showing the cell alignment in a anisotropy way. Figure 2d-e. Macroscopic contraction of collagen gel in about 3mmx3mm square encapsulate with cells in isotropic (e) or anisotropic (d) orientation. Raw images are in folder "Figure 2", subfolder "2f-g_cell_contraction_raw_images", subfolder "2d" and "2e". Figure 2f-g. Normalized width and length over days. w = "width of the collagen sheet", w/w0 = width of the collagen sheet normalized by initial width w0. l = "length of the collagen sheet", l/l0 = length of the collagen sheet normalized by initial length l0. Data set and plots are placed in folder "2f-g_cell_contraction_plot". Raw images are in folder "2f-g_cell_contraction_raw_images". Images from each sample are placed in separate subfolders, and numbered by days. Data are stored in Fig2f.csv and Fig2g.csv. Fig. 3a-3d contain image data, no quantitative data presented. Figure 3a-b. Schematic depicting the cell alignment at different time interval. Figure 3c-d. Microscopy images showing the cell distribution. Figure 3e-f. Angular distribution of the cell nuclei. Data and matlab codes are in folder 3e-f_polarhist. The anisotropy.csv and isotropy.csv files include the nuclei orientation with respect to horizontal axis. The first column labels the nuclei, and the second column is the angle theta for each nuclei. Fig. 3g-i contain image data, no quantitative data presented. Figure 3g-h. Characterization of collagen fibers microscopic structures. Figure 3i. Schematic depicting the collagen alignment and sample preparation for mechanical testing. Figure 3j. Mechanical properties of the collagen samples. Data and matlab codes are in folder "Figure 3", sub folder "3j_elastic_moduli". The code for generating the plot is in matlab script "plot_elastic*moduli.m".* The variable *"std*_modulus" is the standard deviation of the modulus. "Iso/nem" denotes orientation of the substrate, which is the isotropic or nematic substrate.  Fig. 3k contain image data, no quantitative data presented. Figure 3k. Schematic depicting the procedure for force analysis, where cell-cell interation compacts the matrix. Fig. 4a-b contain schematics of the setup, no quantitative data presented. Figure 4a. Schematic of projector display set up. Figure 4b. Schematic depicting the procedure for making hydrogel fiber by photo patterning. Figure 4c-g(i). Schematic depicting the orientation field. Plots are generated by matlab code in folder "Figure 4", subfolder "4c-g(i)_directorfield_plot". For each director field configuration, one uncomments the section associated with defects of a particular charge in matlab script "directorfield_plot.m" Fig. 4c-g(ii)(iii) contain image data, no quantitative data presented. Figure 4c-g(ii). POM images with lamda plate for different photopatterning structure. Figure 4c-g(iii). Phase contrast images of hydrogel fiber. Fig. 5a-c contain image data, no quantitative data presented. Figure 5a-c. Microscopy images of encapsulated cells after seeding on substrate with photopatterning structure. Figure 5d-f. Different shape transformation of cell embedded collagen. The raw images are in folder "Figure 5", subfolder "5d-f_shape_transformation_raw_images".The plot showing orientation are generated by matlab code as Figure 4c-g(i). Figure 6a. Schematic depicting the transformation of cell embedded collagen. The small panel showing the orientation are generated by matlab code as Figure 4c-g(i). Fig. 6b-d contain image data, no quantitative data presented. Figure 6b-c. Microscopy images of encapsulated cells after seeding on substrate with photopatterning structure. Figure 6d. Microscopy images as side view of the dome sample. Figure 6e. Microscopy images of the nuclei channel for dome sample at different depth z in xy plane. The order parameter is obtained by matlab code "orderparametercircularzstack.m" in folder "S14_circular_order_parameter_vs_z". **Supporting Information** Figure S1, S4, S5 S9, and S11-S13 contain only image data. Figure S2 data included in "Figure S2/intensity_vs_chi", where chi denotes the 2D polar angle of and intensity represents the cumulative scattering intensity, which are used to generated the scattering plot. Type denotes the alignment of the substrate, which are either isotropic or nematic.  Figure S3, data included in "Figure S3/figs3.csv", where q denotes the wave vector, and intensity represents the cumulative scattering intensity, which are used to generated the scattering plot. Type denotes the alignment of the substrate. The scattering intensity is obtained either by wide-angle X-ray scattering (WAXS) or small angle X-ray scattering (SAXS).  Figure S6a-d, microscopy images, no quantity data. Figure S6e. Schematic showing the microscopy method, no quantity data. Figure S6f,g Confocal images of the nucleus channel are first binarized, and ellipses are fit to the nuclei, resulting in the csv files representing the orientation of these fit ellipses. The order parameter is computed by loading selective confocal slices and compute the order parameter using the orientation angle extracted by fitting an ellipse to nuclei of the cells contained in that slice, where the number denotes the slice. Figure S6f. Order parameter S plot with depth z. The raw data and code are in folder "S6f_hydrogel_fiber_3D". The order parameter is computed by Matlab script "orderparameterplotz.m". The naming of csv represent the height z at which the analysis is performed. The step size in z is 1 micrometer. For instance, slice "71" represent the orientation of the cell nucleus 71 micron form the top of the sample.  Figure S6g. Order parameter S plot with depth z. The raw data and code are in folder "S6g_LCE_fiber_3D". The order parameter is computed by Matlab script "orderparameterplotz.m". The naming of csv represent the height z at which the analysis is performed. The step size in z is 1 micrometer. For instance, slice "65" represent the orientation of the cell nucleus 71 micron from the top of the sample.  Figure S7. Custom analysis procedure for finding the dimension of collagen matrix. The raw data and code are in folder "S7_anisotropic_contraction_square_fitting". Data points of the boundary (xb,yb) and the fit boundary (xf, yf) are listed in "listingpoints.csv". Figure S8: Data obtained from dynamics mechanical analysis, used to generate the stress vs strain curves are contained in the folder "Figure S8". Figure S10. Shape similarity by fitting different equilateral polygons. The boundary points are taken of the "ShapeXX" (= "Circle1", "Diamond2", or "triangle3") and fit to an equilateral square, triangle, diamond, circle using MATLAB script "fit_shape.m". The plots are generated by matlab script "try_diff_fit_load_geometry". The raw data and code for plotting are included in the folder "Figure S10". Figure S14. Order parameter S plot with depth z for dome sample on circular +1 defect. The raw data and code for plotting are in the folder "Figure S14" where individual slices of csv files denote orientation angle extracted by fitting an ellipse to nuclei of the cells contained in that slice, where the number denotes the slice. The order parameter is computed by Matlab script "orderparametercircularzstack.m" The naming of csv represent the height z at which the analysis is performed. the step size in z is 1 micrometer. For instance, slice "50" represent the orientation of the cell nucleus 50 micron from the top of the sample.  ## Code/software Matlab ## Access information Other publicly accessible locations of the data: n/a Data was derived from the following sources: n/a