This readme file was generated on [2025-02-26] by [OWEN MCGREEVY] GENERAL INFORMATION -------------------------------------------------------------------------------- Title of Dataset: A PRECLINICAL MODEL OF HUMAN LIVER USING PRECISION CUT TISSUE SLICE CULTURE Principal Investigator Information Name: Dr Laura Randle ORCID: https://orcid.org/0000-0002-7881-2979 Institution: University of Liverpool Address: Sherrington Building University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK Email: laura.randle@liverpool.ac.uk Author Information Name: OWEN MCGREEVY ORCID: https://orcid.org/0000-0002-2029-0207 Institution: University of Liverpool Address: Sherrington Building University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK Email: hlomcgre@liverpool.ac.uk Author Information Name: Timothy Gilbert ORCID: https://orcid.org/0000-0003-4821-1897 Institution: University of Liverpool Address: Sherrington Building University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK Email: timothy.gilbert@liverpool.ac.uk Date of data collection: 2023 Geographic location of data collection: Liverpool Information about funding sources that supported the collection of the data: - Funder: NC3Rs (Grant Number NC/X001679) - Funder: North West Cancer Research (NWCR) (Grant Number PHD2022.03) SHARING/ACCESS INFORMATION -------------------------------------------------------------------------------- Licenses/restrictions placed on the data: License: Creative Commons Attribution-Noncommercial-Share Alike 4.0 Was data derived from another source? No Recommended citation for this dataset: McGreevy, O., Gilbert, T., & Randle, L. (2025). _Comparing methods of human precision cut tissue slice culture - tissue slice viability and functional markers data._ (2023-2024). University of Liverpool DataCat. https://datacat.liverpool.ac.uk/id/eprint/2958 DATA & FILE OVERVIEW -------------------------------------------------------------------------------- File List: 1. File Name: Viability Data NC3Rs paper.xlsx - Visibility: Anyone - Content type: Data - Description: MTS viability data for human precision cut tissue slices (hPCTS) cultured over 15 days using three different culture methods (no insert, Millicell insert, CELLBLOCKS®). - Mime-Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet - File size: ~51 kB - License: Creative Commons Attribution-Noncommercial-Share Alike 4.0 2. File Name: Urea and Albumin Data NC3Rs paper.xlsx - Visibility: Anyone - Content type: Data - Description: Percentage change in urea and albumin secretion into media from day 3 in hPCTS cultured over 15 days. - Mime-Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet - File size: ~19 kB - License: Creative Commons Attribution-Noncommercial-Share Alike 4.0 Relationship between files, if important: - Both files come from the same study. The first (Viability Data NC3Rs) measures viability via MTS assays, while the second (Urea and Albumim Data NC3Rs) measures functional markers (urea and albumin) secreted by the tissue slices. Are there multiple versions of the dataset? No. METHODOLOGICAL INFORMATION -------------------------------------------------------------------------------- Description of methods used for collection/generation of data: 1. **Patient selection and tissue collection** - Liver tissue was collected from 5 patients undergoing surgery for a liver tumor at the Royal Liverpool University Hospital. - Ethical approval was obtained under NIHR PINCER (NW REC 15/NW/0477). - Normal liver tissue was placed in University of Wisconsin (UW) buffer and transferred on ice to the laboratory within 1 hour. 2. **Culture Conditions**: - Three culture systems were tested over 15 days: 1) 24-well plate (no insert) 2) Millicell standing inserts (PTFE membrane) 3) CELLBLOCKS® (hydrophilic PET flow system) - Culture media was changed on Day 1 and every 48 hours thereafter. - Slices were maintained at 37°C, 5% CO₂, with mild agitation (orbital or rocking platform). 3.**Viability Assay (MTS)**: - MTS assays (CellTiter 96® Aqueous One Solution) were conducted on Days 0, 3, 7, 11, and 15. - Absorbance was measured at 490 nm after 3 hours incubation with MTS reagent. 4.**Urea & Albumin Quantification**: - Media samples were collected at Days 3, 7, and 15. - Urea was measured using a colorimetric Urea Assay kit (Abcam), and albumin was measured using a Human Albumin ELISA kit (Abcam), both following the manufacturer’s instructions. 5.**Data Analysis & Statistics**: - Raw MTS absorbance values were normalized to Day 0 (=100%). - Urea and albumin measurements are expressed as percentage change relative to Day 3 levels. - GraphPad Prism (v10.0.3) was used for mixed-effects or RM-ANOVA analysis with Dunnett’s post-hoc tests. - Missing data (e.g., infected slices) were removed from analyses. Methods for processing the data: - Normalization of MTS absorbance to the Day 0 baseline. - Calculation of percentage changes in albumin and urea from Day 3 levels. - Outlier and contaminated slice exclusion. Instrument- or software-specific information needed to interpret the data: - Krumdieck MD6000 tissue microtome settings (arm speed 4, blade speed 4). - GraphPad Prism version 10.0.3 for statistical analysis. -Varioskan Flash 2.4.5 - Thermo Scientific - plate reader Standards and calibration information, if appropriate: - All colorimetric and ELISA kits were run with provided standards. Environmental/experimental conditions: - All cultures were maintained at 37°C, 5% CO₂, and media was agitated at 95 rpm or with a rocking platform. Describe any quality-assurance procedures performed on the data: - Technical replicates of each slice and pooled media for functional markers. - Slices showing signs of infection or damage were excluded. People involved with sample collection, processing, analysis and/or submission: - Owen McGreevy - Timothy Gilbert - Laura Randle DATA-SPECIFIC INFORMATION FOR: Viability Data NC3Rs paper.xlsx -------------------------------------------------------------------------------- Number of variables: 3 conditions 5 biological replicates Number of cases/rows: 5 timepoints Variable List: - Sample: 606 2706 1807 2807 609 - Culture_System: {No Insert (NI) , Millicell Insert (I), CELLBLOCKS (RC)} - Timepoint: {Day 0, 3, 7, 11, 15} - Raw_Absorbance: MTS absorbance at 490 nm - Viability_Percent: Percentage viability normalized to Day 0 = 100% Missing data codes: - NA: indicates excluded or missing measurement Specialized formats or other abbreviations used: - hPCTS: human Precision Cut Tissue Slices - MTS: CellTiter 96® Aqueous One Solution assay - PTFE: polytetrafluoroethylene - PET: polyethylene terephthalate DATA-SPECIFIC INFORMATION FOR: Urea and Albumin Data NC3Rs paper.xlsx -------------------------------------------------------------------------------- Number of variables: 3 conditions 5 biological replicates Number of cases/rows: 4 timepoints for Albumin 3 timepoints for Urea Variable List: - Sample 606 2706 1807 2807 609 - Culture_System: {No Insert (NI) , Millicell Insert (I), CELLBLOCKS (RC)} - Timepoint: Ablumin {Day 3, 7, 11, 15} Urea {Day 3, 7, 15} - Albumin_Change_Percent: Albumin concentration expressed as % change from Day 3 - Urea_Change_Percent: Urea concentration expressed as % change from Day 3 Missing data codes: - NA: indicates excluded or missing measurement This readme file was generated on 2025-02-26 by OWEN MCGREEVY GENERAL INFORMATION -------------------------------------------------------------------------------- Title of Dataset: A PRECLINICAL MODEL OF HUMAN LIVER USING PRECISION CUT TISSUE SLICE CULTURE Principal Investigator Information Name: Dr Laura Randle ORCID: https://orcid.org/0000-0002-7881-2979 Institution: University of Liverpool Address: Sherrington Building, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK Email: laura.randle@liverpool.ac.uk Author Information Name: OWEN MCGREEVY ORCID: https://orcid.org/0000-0002-2029-0207 Institution: University of Liverpool Address: Sherrington Building, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK Email: hlomcgre@liverpool.ac.uk Author Information Name: Timothy Gilbert ORCID: https://orcid.org/0000-0003-4821-1897 Institution: University of Liverpool Address: Sherrington Building, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK Email: timothy.gilbert@liverpool.ac.uk Date of data collection: 2023 Geographic location of data collection: Liverpool Information about funding sources that supported the collection of the data: - Funder: NC3Rs (Grant Number: NC/X001679) - Funder: North West Cancer Research (NWCR) (Grant Number: PHD2022.03) SHARING/ACCESS INFORMATION -------------------------------------------------------------------------------- Licenses/restrictions placed on the data: Creative Commons Attribution-Noncommercial-Share Alike 4.0 Was data derived from another source? No Recommended citation for this dataset: McGreevy, O., Gilbert, T., & Randle, L. (2025). _Comparing methods of human precision cut tissue slice culture - tissue slice viability and functional markers data._ (2023-2024). University of Liverpool DataCat. https://datacat.liverpool.ac.uk/id/eprint/2958 DATA & FILE OVERVIEW -------------------------------------------------------------------------------- File List: 1. File Name: Viability Data NC3Rs paper.xlsx - Visibility: Anyone - Content type: Data - Description: MTS viability data for human precision cut tissue slices (hPCTS) cultured over 15 days using three different culture methods (no insert, Millicell insert, CELLBLOCKS®). - Mime-Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet - File size: ~51 kB - License: Creative Commons Attribution-Noncommercial-Share Alike 4.0 2. File Name: Urea and Albumin Data NC3Rs paper.xlsx - Visibility: Anyone - Content type: Data - Description: Percentage change in urea and albumin secretion into media from Day 3 in hPCTS cultured over 15 days. - Mime-Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet - File size: ~19 kB - License: Creative Commons Attribution-Noncommercial-Share Alike 4.0 Relationship between files, if important: - Both files come from the same study. The first (Viability Data NC3Rs) measures viability via MTS assays, while the second (Urea and Albumin Data NC3Rs) measures functional markers (urea and albumin) secreted by tissue slices. Are there multiple versions of the dataset? No. METHODOLOGICAL INFORMATION -------------------------------------------------------------------------------- Description of methods used for collection/generation of data: 1. **Patient selection and tissue collection** - Liver tissue was collected from 5 patients undergoing surgery for a liver tumor at the Royal Liverpool University Hospital. - Ethical approval was obtained under NIHR PINCER (NW REC 15/NW/0477). - Normal liver tissue was placed in University of Wisconsin (UW) buffer and transferred on ice to the laboratory within 1 hour. 2. **Culture Conditions** - Three culture systems were tested over 15 days: 1) 24-well plate (no insert) 2) Millicell standing inserts (PTFE membrane) 3) CELLBLOCKS® (hydrophilic PET flow system) - Culture media was changed on Day 1 and every 48 hours thereafter. - Slices were maintained at 37°C, 5% CO₂, with mild agitation (orbital or rocking platform). 3. **Viability Assay (MTS)** - MTS assays (CellTiter 96® Aqueous One Solution) were conducted on Days 0, 3, 7, 11, and 15. - Absorbance was measured at 490 nm after 3 hours incubation with MTS reagent. 4. **Urea & Albumin Quantification** - Media samples were collected at Days 3, 7, and 15. - Urea was measured using a colorimetric Urea Assay kit (Abcam), and albumin was measured using a Human Albumin ELISA kit (Abcam), both following the manufacturer’s instructions. 5. **Data Analysis & Statistics** - Raw MTS absorbance values were normalized to Day 0 (=100%). - Urea and albumin measurements are expressed as percentage change relative to Day 3 levels. - GraphPad Prism (v10.0.3) was used for mixed-effects or RM-ANOVA analysis with Dunnett’s post-hoc tests. - Missing data (e.g., infected slices) were removed from analyses. Methods for processing the data: - Normalization of MTS absorbance to the Day 0 baseline. - Calculation of percentage changes in albumin and urea from Day 3 levels. - Outlier and contaminated slice exclusion. Instrument- or software-specific information needed to interpret the data: - Krumdieck MD6000 tissue microtome (arm speed 4, blade speed 4). - GraphPad Prism version 10.0.3 for statistical analysis. - Varioskan Flash 2.4.5 – Thermo Scientific plate reader. Standards and calibration information, if appropriate: - All colorimetric and ELISA kits were run with provided standards. Environmental/experimental conditions: - All cultures were maintained at 37°C, 5% CO₂, with media agitated at 95 rpm or via a rocking platform. Describe any quality-assurance procedures performed on the data: - Technical replicates of each slice and pooled media for functional markers. - Slices showing signs of infection or damage were excluded. People involved with sample collection, processing, analysis and/or submission: - Owen McGreevy - Timothy Gilbert - Laura Randle DATA-SPECIFIC INFORMATION FOR: Viability Data NC3Rs paper.xlsx -------------------------------------------------------------------------------- Number of variables: - 3 culture conditions, 5 biological replicates Number of cases/rows: - 5 timepoints (Day 0, 3, 7, 11, 15) Variable List: - Sample: 606, 2706, 1807, 2807, 609 - Culture_System: {No Insert (NI), Millicell Insert (I), CELLBLOCKS (RC)} - Timepoint: {Day 0, Day 3, Day 7, Day 11, Day 15} - Raw_Absorbance: MTS absorbance at 490 nm - Viability_Percent: Percentage viability normalized to Day 0 = 100% Missing data codes: - NA: indicates excluded or missing measurement Specialized formats or other abbreviations used: - hPCTS: human Precision Cut Tissue Slices - MTS: CellTiter 96® Aqueous One Solution assay - PTFE: polytetrafluoroethylene - PET: polyethylene terephthalate DATA-SPECIFIC INFORMATION FOR: Urea and Albumin Data NC3Rs paper.xlsx -------------------------------------------------------------------------------- Number of variables: - 3 culture conditions, 5 biological replicates Number of cases/rows: - Albumin measured at 4 timepoints (Day 3, 7, 11, 15) - Urea measured at 3 timepoints (Day 3, 7, 15) Variable List: - Sample: 606, 2706, 1807, 2807, 609 - Culture_System: {No Insert (NI), Millicell Insert (I), CELLBLOCKS (RC)} - Timepoint (Albumin): {Day 3, Day 7, Day 11, Day 15} - Timepoint (Urea): {Day 3, Day 7, Day 15} - Albumin_Change_Percent: Albumin concentration as % change from Day 3 - Urea_Change_Percent: Urea concentration as % change from Day 3 Missing data codes: - NA: indicates excluded or missing measurement Specialized formats or other abbreviations used: - UW buffer = University of Wisconsin buffer END OF README Specialized formats or other abbreviations used: - Additional abbreviations: UW buffer = University of Wisconsin buffer END OF README