This readme file was generated on 2024-11-27 and updated on 2024-12-01 by Eleanor L.P. Caston. This document serves as the metadata for all supporting files to the manuscript "Engineering the Microstructure and Spatial Bioactivity of MAP Scaffolds Instructs Vasculogenesis In Vitro and Modifies Vessel Formation In Vivo " (2024, Advanced Functional Materials). Resources (raw data, analyzed data sets) beyond those in the main article and supplemental information are available here in accordance with the published NIH guidelines (https://sharing.nih.gov/) for the dissemination of all research resources related to projects under NIH funding. All data will be stored and accessible through Duke University's public repository (https://research.repository.duke.edu/). Physical materials may be made available to the non-commercial research community upon request and acceptance of terms under Duke's Material Transfer Agreements. GENERAL INFORMATION Title of Dataset: Data from: Engineering the Microstructure and Spatial Bioactivity of MAP Scaffolds Instructs Vasculogenesis In Vitro and Modifies Vessel Formation In Vivo Author Information Name: Alexa Anderson, orcid.org/0000-0002-8566-4310 Institution: Duke University (Biomedical Engineering) Address: 534 Research Drive, Wilkinson Bldg, Rm 330, Durham, NC 27708 Email: alexa.anderson@duke.edu Principal Investigator Name: Tatiana Segura, Ph.D. ORCID: 0000-0003-1569-8686 Institution: Duke University (Biomedical Engineering) Address: 534 Research Drive, Wilkinson Bldg, Rm 330, Durham, NC 27708 Email: tatiana.segura@duke.edu Date of data collection: 2022-2023 Geographic location of data collection: Durham, NC, USA Funding sources: This work was made possible with government support under Federal Grant No. R01NS112940 awarded by the National Institutes of Health. SHARING/ACCESS INFORMATION Links to publications that cite or use the data: 10.1002/adfm.202400567 Duke Research Data Repository. https://doi.org/10.7924/r4wm1hb9r DATA & FILE OVERVIEW The folder structure is grouped by each Figure with the data corresponding to each panel/plot in the respective subfolder. Data acquired from images is provided in Excel (.XLSX) format or CSV format. PRISM files used for analysis and plotting are included for full disclosure. ND2 files of confocal microscopy images are included for biological (labeled as "N") and technical replicates (labeled as "n"). JPG or TIFF images are only included for the representative images present in the manuscript. Naming convention: Each file name (as appropriate) has the condition name, the timepoint, the biological/technical replicate (labeled as "N"), the technical replicates (labeled as "n"), the date of data generation, the figure it refers to, the objective used (ie 20X), and the stains represented by the channels. For example: 121422_N1_n1_Day3_ECFC_50 RGD488_50 nHRGD555_DAPIphal_20x means the data was collected on Dec 14, 2022. It is the first technical replicate of the first biological replicate. It was data from day 3 of the study with ECFCs (endothelial colony forming cells). It is a 50 RGD50 nHRGD condition with RGD on the 488 channel and nH RGD on the 555 channel. It also has DAPI and phalloidin. And it was taken on 20X. METHODOLOGICAL INFORMATION Please refer to the publication for detailed methods. Description of methods used for collection/generation of data: Figures 2, 3, 4, 5, 6, 7 and 8 have data collected via confocal microscopy imaging. Figure 3H-J has data generated in MATLAB. Figure 3K-N and Figure 4H-O has data generated using methods from Riley, L., Wei, G., Bao, Y., Cheng, P., Wilson, K.L., Liu, Y., Gong, Y. and Segura, T. (2023), Void Volume Fraction of Granular Scaffolds. Small, 19: 2303466.Êhttps://doi.org/10.1002/smll.202303466. Figure 7G has data generated from IHC stained sections. Image analysis of MAP scaffolds: In IMARIS software, the spot counter tool was used to quantify the number of ?gels as well as identify their X, Y, and Z coordinates for each population using the corresponding fluorescent signal. A custom MATLAB script was written to calculate the distance between ?gels using the X, Y, and Z coordinates and determine the distance to the nearest ?gel. Another custom MATLAB script was written to analyze the fluorescence of each ?gel population within 150 ?m x 150 ?m x 150 ?m volumes throughout the Z-stack. Image analysis of cell response: In IMARIS software, 3D volume renderings of confocal Z-stacks were used to quantify cell volume (F-actin) and scaffold volume. The IMARIS spot counter tool was used to quantify cell counts using DAPI signal. Number of vacuoles were quantified manually in ImageJ. The ImageJ plugin DiaAna was used to quantify colocalization of nuclei (DAPI signal) with fluorescently labeled µgel populations. The ImageJ Angiogenesis Analyzer plugin was used to assess network length and branches. ImageJ was used to quantify % area of the fluorescent channel for each extracellular matrix component. Wound healing analysis: The colocalization of CD31 and NG-2 fluorescence was quantified using Just Another Colocalization Plugin (JaCoP) in ImageJ.[44] ). IHC Images were analyzed using HALO (Indica Labs). The Indica Labs - Area Quantification v2.4.3 plugin was used to identify DAB positive areas for each wound region to give %DAB positive. Software- or Instrument-specific information needed to interpret the data, including software version numbers, packages or other dependencies: All raw data is provided for interpretation in accessible formats. But, IMARISx64 and ImageJ with the DiaAna and Angiogensis Analyzer plugins will be needed to reanalyze the ND2 files provided. Additionally, HALO software is needed to re-analyze IHC images from figure 7. Standards and calibration information, if appropriate: N/A Environmental/experimental conditions: Experimental conditions were in a controlled environment in a Duke laboratory.