ReadMe file for NAFLD Animal Models Database v1 Contact: Jake Mann, Institute of Metabolic Science, Cambridge, UK jm2032@cam.ac.uk Data used in a manuscript currently under review. Derived from a systematic review of rodent models of NAFLD. Data representes the raw data and references to all included studies. Search completed January 2019. Data updated November 2020. The dataset is two tabs in a .xlsx file. The first tab "Papers & refs" gives the references for each article included in the review. The second tab "Models" provides full details of each model included in the review. The data is free to use with no restrictions. Full description of the analysis, methods, and processing of the data will be available in the manuscript once published. The code used for analysis (with R 4.0.2) accompanies this dataset and ReadMe. Note that for analysis Tab1 ('Papers & refs') needs to separated and renamed as "AnMod_papers_Nov20_v2.xlsx"; and Tab2 ('Models') needs to be separated and renamed as "AnMod_models_Nov20_v2.xlsx". Variable list: Tab1 "Papers & refs" ID - Unique study ID. This relates to column BP in the "Models" tab and is used as a the 'Reference ID number' Study - Surname and Year of the article Year - Year article was published Title - Title of the article included Include - Include/Exclude against the review's criteria. [Note that excluded studies have not been included in this dataset.] Models - The model(s) used by each study. If there are multiple models this will result in multiple rows per study. Background - Genetic background used in each model. Paper_type - The paper type, categorised as: Phase 2/3 (i.e. an interventional study using an agent also used in phase 2/3 trials in humans), Mechanistic, Model description, Interventional (other) (i.e. an interventional study not covered by Phase 2/3), or Other Other - The agent used as part of 'Interventional (other)' studies Gene1 - Key gene1 reported in the abstract of the paper Gene2 - Key gene2 reported in the abstract of the paper Gene3 - Key gene3 reported in the abstract of the paper Other mechanistic factor - Any other mechanistic factor reported in the abstract of the paper Tx_omic - GEO dataset GSE code (to be used at: https://www.ncbi.nlm.nih.gov/gds) for transcriptomic data Protocol - Presence of a protocol Randomisation - Use of randomisation Blinding - Use of blinding Power_calc - Description of a power calculation or sample size estimation Qual_score - Score (0-4) using the previous four risk of bias items Tab2 "Models" Category - Overall category of the model Main_group - Main group of the model Gene - Murine gene involved in genetically modified animals HUGO_gene - Human ortholog in HUGO format for genetic models Subgroup - Subgroup for each model Detail - Description/nomenclature of the model as used by the article (i.e. this has not been edited/curated by us) Background - Full/long genetic background of the model Background_simple - Simplified/grouped genetic background Sex - Sex of animals used Diet_detail - Age (weeks of life) of when the diet was initiated (blank if not stated) Diet_num - Age (weeks of life) of when the diet was initiated (blank if not stated) [formatted as number for analysis] Fat_detail - Proportion of fat in diet (%kcal) Fat_num - Proportion of fat in diet (%kcal) [formatted as number for analysis] Cholest_per - Proportion of cholesterol in diet (%weight) Cholest_num - Proportion of cholesterol in diet (%weight) [formatted as number for analysis] Choline_num - Proportion of choline in diet (%weight) [formatted as number for analysis] Sucrose_kcal - Proportion of sucrose in diet (%kcal) Sucrose_num - Proportion of sucrose in diet (%kcal) [formatted as number for analysis] Fruct_wt - Proportion of fructose in diet (%weight) Fruct_water_solid - Whether fructose was provided as solid or liquid/in water Fruct_water_num - Proportion of fructose in diet (%weight) where included in water or as a liquid Fruct_num - Proportion of fructose in diet (%weight) [formatted as number for analysis] Fruct_solid_num - Proportion of fructose in diet (%weight) where included as solid diet Chem_age - Age that a chemical or surgical intervention was made (in weeks), also to include age that viral agents were given in genetically modified animals Chem_age_num - Age that a chemical or surgical intervention was made (in weeks), also to include age that viral agents were given in genetically modified animals [formatted as number for analysis] Chem_dose - Dose of chemical agents Chem_route_full - Full/long route of chemical dose administration Chem_route_simple - Simplified/grouped route of chemical administration Lipodyst - Presence of lipodystrophy (Yes/no) Obesity - Reported presence of obesity (Yes/No/? (unclear)/blank) - left blank if not stated. Yes=statistically greater weight (or fat mass) in model than control animals. Insul_res - Reported presence of insulin resistance (Yes/No/? (unclear)/blank) - left blank if not stated. Yes=statistically higher fasting/post-prandial insulin or glucose in model than control animals. Dyslip - Reported presence of dyslipidaemia (Yes/No/? (unclear)/blank) - left blank if not stated. Yes=statistically higher triglycerides/low density lipoprotein/cholesterol or lower high density lipoportein in model than control animals. Metab_score - Metabolic syndrome score (0-3) from the previous three items Liver_score - Liver histology score (0-11) from the subsequent 11 times NAFLD_score - Sum of metabolic and liver scores (0-14) Transamin - Reported presence of raised transaminases (Yes/No/? (unclear)/blank) - left blank if not stated. Yes=statistically higher alanine or aspartate aminotransferase in model than control animals. Balloon_YN - Reported presence of hepatocellular ballooning at any time point (Yes/No/? (unclear)/blank) - left blank if not stated NASH_YN - Reported presence of steatohepatitis at any time point (Yes/No/? (unclear)/blank) - left blank if not stated Lobul_YN - Reported presence of lobular inflammation at any time point (Yes/No/? (unclear)/blank) - left blank if not stated Portal_YN - Reported presence of (peri-)portal inflammation at any time point (Yes/No/? (unclear)/blank) - left blank if not stated Fib_YN - Reported presence of fibrosis of any stage at any time point (Yes/No/? (unclear)/blank) - left blank if not stated Fib_F1 - Reported presence of at least stage 1 fibrosis (Yes/No/? (unclear)/blank) - left blank if not stated Fib_F2 - Reported presence of at least stage 2 fibrosis (Yes/No/? (unclear)/blank) - left blank if not stated Fib_F3 - Reported presence of at least stage 3 fibrosis (Yes/No/? (unclear)/blank) - left blank if not stated Fib_F4 - Reported presence of at least stage 4 fibrosis (Yes/No/? (unclear)/blank) - left blank if not stated HCC_YN - Reported presence of hepatocellular carcinoma at any time point (Yes/No/? (unclear)/blank) - left blank if not stated Fib_stage - Maximum fibrosis stage reported for the model (or Yes_NR if stated to show fibrosis but stage not described) HepTrig - Reported presence of elevated quantitatively measured hepatic triglyceride content (Yes/No/? (unclear)/blank) - left blank if not stated. Yes=statistically higher hepatic triglyceride in model than control animals. Steat_YN - Reported presence of hepatic steatosis (Yes/No/? (unclear)/blank) - left blank if not stated. Steat_wk - Timings (in weeks) that steatosis was described in the model Steat_max - Maximum age (in weeks) that the presence of steatosis was described for this model Balloon_wk - Timings (in weeks) that ballooning was described in the model Balloon_max - Maximum age (in weeks) that the presence of ballooning was described for this model NASH_wk - Timings (in weeks) that steatohepatitis was described in the model NASH_max - Maximum age (in weeks) that the presence of steatohepatitis was described for this model Lobul_wk - Timings (in weeks) that lobular inflammation was described in the model Lobul_max - Maximum age (in weeks) that the presence of lobular inflammation was described for this model Portal_wk - Timings (in weeks) that portal inflammation was described in the model Portal_max - Maximum age (in weeks) that the presence of portal inflammation was described for this model Fib_wk - Timings (in weeks) that fibrosis was described in the model Fib_max - Maximum age (in weeks) that the presence of fibrosis was described for this model HCC_wk - Timings (in weeks) that hepatocellular carcinoma was described in the model HCC_max - Maximum age (in weeks) that the presence of hepatocellular carcinoma was described for this model Timing_wk - How to interpret the 'timings (weeks)' in this row (model). Usually as number of weeks after diet was started ('Diet') or week of life ('Life'). Ref_det - The IDs of the individual studies that utilised this model (see column A in tab 1) Ref_no - The number of studies using this model Comments - Additional comments