READ ME File For 'Supplementary videos of the thesis "Individual and Collective Mechanosensing of Extracellular Matrix Thickness in Skeletal Stem Cell Differentiation"' Dataset DOI: 10.5258/SOTON/D2640 Date that the file was created: May, 2023 ------------------- GENERAL INFORMATION ------------------- ReadMe Author: MARIA LUISA HERNANDEZ MIRANDA, University of Southampton [0000-0002-7366-898X] Date of data collection: 1st October 2023-8th October 2023 Information about geographic location of data collection: Southampton, UK Related projects: “Individual and Collective Mechanosensing of Extracellular Matrix Thickness in Skeletal Stem Cell Differentiation” -------------------------- SHARING/ACCESS INFORMATION -------------------------- Licenses/restrictions placed on the data, or limitations of reuse: CC BY Recommended citation for the data: Hernandez-Miranda (2023). “Individual and Collective Mechanosensing of Extracellular Matrix Thickness in Skeletal Stem Cell Differentiation”. Thesis. University of Southampton. This dataset supports the publication: AUTHORS: Hernandez-Miranda M, Xu D, Johnston DA, Browne M, Cook RB, Sengers BG2, Evans ND TITLE: “Geometric constraint of mechanosensing in marrow stromal cell cultures prevents stiffness-induced differentiation.” JOURNAL: in progress PAPER DOI IF KNOWN: in progress Links to other publicly accessible locations of the data: Links/relationships to ancillary or related data sets: -------------------- DATA & FILE OVERVIEW -------------------- This dataset contains: 39 videos [File list (filenames, directory structure (for zipped files) and brief description of all data files)] Supplementary Video 1a: 1kPa 25µL 1h BF. Supplementary Video 1b: 1kPa 25µL 1h Cy3. Supplementary Video 2a: 40 kPa 25µL A 1h BF. Supplementary Video 2b: 40 kPa 25µL 1h Cy3. Supplementary Video 3a: 1kPa 5µL 1 h BF. Supplementary Video 3b: 1kPa 5µL 1h Cy3. Supplementary Video 4a: 40 kPa 5µL 1h BF. Supplementary Video 4b: 40 kPa 5µL 1h Cy3. Supplementary Video 5a: 1kPa 25µL day 10 BF. Supplementary Video 5b: 1 kPa 5µL day 10 BF. Supplementary Video 6a: 1kPa 25µL day 10 Cy3. Supplementary Video 6b: 1 kPa 5µL day 10 Cy3. Supplementary Video 7a: 40kPa 25µL day 10 BF. Supplementary Video 7b: 40kPa 5µL day 10 BF. Supplementary Video 8a: 40kPa 25µL day 10 Cy3. Supplementary Video 8b: 40kPa 5µL day 10 Cy3. Supplementary Video 9a: 1kPa 25µL week 7 BF. Supplementary Video 9b: 1kPa 5µL week 7 BF. Supplementary Video 10a: 1kPa 25µL week 7 Cy3. Supplementary Video 10b: 1kPa 5µL week 7 Cy3. Supplementary Video 11a: Basal 1,000 cells BF. Supplementary Video 11b: Basal 5,000 cells BF. Supplementary Video 11c: Basal 10,000 cells BF. Supplementary Video 11d: Basal 20,000 cells BF. Supplementary Video 12a: Osteogenic 1,000 cells BF. Supplementary Video 12b: Osteogenic 5,000 cells BF. Supplementary Video 12c: Osteogenic 10,000 cells BF. Supplementary Video 12d: Osteogenic 20,000 cells BF. Supplementary Video 13a: Basal 1KPa 5µL 1,000 cells day 1 BF. Supplementary Video 13b: Osteogenic 1KPa 5µL 1,000 cells day 1 BF. Supplementary Video 14a: Basal 1KPa 5µL 5,000 cells day 1 BF. Supplementary Video 14b: Osteogenic 1KPa 5µL 5,000 cells day 1 BF. Supplementary Video 15a: Basal 1KPa 25µL 1,000 cells day 1 BF. Supplementary Video 15b: Osteogenic 1KPa 25µL 1,000 cells day 1 BF. Supplementary Video 16a: Basal 1KPa 25µL 5,000 cells day 1 BF. Supplementary Video 16b: Osteogenic 1KPa 25µL 5,000 cells day 1 BF. Supplementary Video 17a: Basal 1KPa 25µL 1,000 cells day 14 BF. Supplementary Video 17b: Osteogenic 1KPa 25µL 1,000 cells day 14 BF. Supplementary Video 18a: 40kPa micropatterned hydrogels with 100µm wells. Relationship between files, if important for context: The videos provide more information to the reader and support the figures stated in the thesis. Additional related data collected that was not included in the current data package: Original ND2 files containing all the images of each time-lapse experiment If data was derived from another source, list source: If there are there multiple versions of the dataset, list the file updated, when and why update was made: -------------------------- METHODOLOGICAL INFORMATION -------------------------- Description of methods used for collection/generation of data: The time-lapse videos were obtained using a Nikon Eclipse Ti inverted microscope. The cells were plated on hydrogels with different mechanical properties and under different conditions (seeding density and/or media conditions, and recorded at different time points. Methods for processing the data: The software in the microscope produced (after each experiment) a big ND2 file. I extracted the images, divided them into different files (for each condition) and analyse the data in MATLAB using the functions detailed in the thesis as Appendix A and B. These functions (Zarkoob et al., 2015) were modified and adjusted with the help of Dr Bram Sengers (supervisor and contributor). The data obtained from MATLAB were analysed in graphpad. Software- or Instrument-specific information needed to interpret the data, including software and hardware version numbers: MATLAB R2021a, GraphPad Prism 9. Standards and calibration information, if appropriate: Environmental/experimental conditions: Describe any quality-assurance procedures performed on the data: Different tests were run to ensure the parameters of the analysis were correct, and the background noise was also removed by the modifications made to the MATLAB functions as they only consider displacements for low cell number People involved with sample collection, processing, analysis and/or submission: Maria Luisa Hernandez Miranda, Bram Sengers -------------------------- DATA-SPECIFIC INFORMATION -------------------------- Number of variables: Number of cases/rows: Variable list, defining any abbreviations, units of measure, codes or symbols used: Missing data codes: Specialized formats or other abbreviations used: Abbreviations: kPa=kilopascals (Hydrogel elastic modulus), µL=microliters (Hydrogel thickness; 5µL defined as thin and 25µL defined as thick), h=hours, BF=Brightfield (phase-contrast images); Cy3=Cy3 Channel (fluorescent images), cm2= centimetre (cell number/area). Variables Supplementary Video 1a: 1kPa 25µL 1h BF. 2 Supplementary Video 1b: 1kPa 25µL 1h Cy3. 2 Supplementary Video 2a: 40 kPa 25µL A 1h BF. 2 Supplementary Video 2b: 40 kPa 25µL 1h Cy3. 2 Supplementary Video 3a: 1kPa 5µL 1 h BF. 2 Supplementary Video 3b: 1kPa 5µL 1h Cy3. 2 Supplementary Video 4a: 40 kPa 5µL 1h BF. 2 Supplementary Video 4b: 40 kPa 5µL 1h Cy3. 2 Supplementary Video 5a: 1kPa 25µL day 10 BF. 2 Supplementary Video 5b: 1 kPa 5µL day 10 BF. 2 Supplementary Video 6a: 1kPa 25µL day 10 Cy3. 2 Supplementary Video 6b: 1 kPa 5µL day 10 Cy3. 2 Supplementary Video 7a: 40kPa 25µL day 10 BF. 2 Supplementary Video 7b: 40kPa 5µL day 10 BF. 2 Supplementary Video 8a: 40kPa 25µL day 10 Cy3. 2 Supplementary Video 8b: 40kPa 5µL day 10 Cy3. 2 Supplementary Video 9a: 1kPa 25µL week 7 BF. 2 Supplementary Video 9b: 1kPa 5µL week 7 BF. 2 Supplementary Video 10a: 1kPa 25µL week 7 Cy3. 2 Supplementary Video 10b: 1kPa 5µL week 7 Cy3. 2 Supplementary Video 11a: Basal 1,000 cells BF. 2 Supplementary Video 11b: Basal 5,000 cells BF. 2 Supplementary Video 11c: Basal 10,000 cells BF. 2 Supplementary Video 11d: Basal 20,000 cells BF. 2 Supplementary Video 12a: Osteogenic 1,000 cells/cm2 BF. 2 Supplementary Video 12b: Osteogenic 5,000 cells BF. 2 Supplementary Video 12c: Osteogenic 10,000 cells BF. 2 Supplementary Video 12d: Osteogenic 20,000 cells BF. 2 Supplementary Video 13a: Basal 1KPa 5µL 1,000 cells day 1 BF. 3 Supplementary Video 13b: Osteogenic 1KPa 5µL 1,000 cells day 1 BF. 4 Supplementary Video 14a: Basal 1KPa 5µL 5,000 cells day 1 BF. 4 Supplementary Video 14b: Osteogenic 1KPa 5µL 5,000 cells day 1 BF. 4 Supplementary Video 15a: Basal 1KPa 25µL 1,000 cells day 1 BF. 4 Supplementary Video 15b: Osteogenic 1KPa 25µL 1,000 cells day 1 BF. 4 Supplementary Video 16a: Basal 1KPa 25µL 5,000 cells day 1 BF. 4 Supplementary Video 16b: Osteogenic 1KPa 25µL 5,000 cells day 1 BF. 4 Supplementary Video 17a: Basal 1KPa 25µL 1,000 cells day 14 BF. 4 Supplementary Video 17b: Osteogenic 1KPa 25µL 1,000 cells day 14 BF. 4 Supplementary Video 18a: 40kPa micropatterned hydrogels with 100µm wells. 1