DOI: 10.5061/dryad.9zw3r22kt
title: Data From: Global huntingtin knockout in adult mice leads to fatal neurodegeneration that spares the pancreas

description: Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by
 an expanded CAG tract in the Huntingtin (HTT) gene, leading to toxic gains
 of function. HTT-lowering treatments are in clinical trials but risks
 imposed are unclear. Recent studies have reported on the consequences of
 widespread HTT loss in mice, where one group described early HTT loss
 leading to fatal pancreatitis, but later loss as benign. Another group
 reported no pancreatitis but found widespread neurological phenotypes
 including subcortical calcification. To better understand the liabilities
 of widespread HTT loss we knocked out Htt with two separate
 tamoxifen-inducible Cre lines. We find that loss of HTT at 2 months of age
 leads to progressive tremors and severe subcortical calcification at
 examination at 14 months of age but does not result in acute pancreatitis
 or histological changes in the pancreas. We additionally report that HTT
 loss is followed by sustained induction of circulating neurofilament light
 chain levels. These results confirm that global loss of HTT in mice is
 associated with pronounced risks, including progressive subcortical
 calcification and neurodegeneration.
description: Data and R scripts from the manuscript: Global huntingtin
 knockout in adult mice leads to fatal neurodegeneration that spares the
 pancreas (https://doi.org/10.26508/lsa.202402571)
description: # Data From: Replication Study: Adult-Onset, Global Huntingtin Knockout in
 Mice Leads to Fatal Progressive Neurodegeneration but not Pancreatic
 Pathology
 [https://doi.org/10.5061/dryad.9zw3r22kt](https://doi.org/10.5061/dryad.9zw3r22kt) Dataset and R scripts used to generate all statistics and figures for the associated manuscript are deposited here in the .xlsx file 'cKO manuscript rProject source data.xlsx'. The .xlsx file comprises 17 separate worksheets with a leading number (e.g. 01b, 01c, etc) which indicates where the data was used in the manuscript, along with a short identifying text (e.g. Sentinel HTT) which gives additional context about what the data corresponds to. Each worksheet and it's column headings are defined below.  Corresponding R scripts for analysis are also included. R scripts pull data from the .xlsx sheet and make plots and/or run statistics used in the manuscript and include basic annotation. R script naming follows the same convention as the data, for example the script '01b - Sentinel Study HTT Levels.R' is the script that plots and analyzes the data underlying Figure 01B in the manuscript. ### Descriptions | **Sheet** | **Column header** | **Definition** | | :------------------ | :----------------------------------- | :----------------------------------------------------------------------------------- | | 01b - Sentinel HTT | Pedigree.Number | Individual Mouse Identification number | | 01b - Sentinel HTT | geno | Mouse genotype | | 01b - Sentinel HTT | sac.month | age at tissue collection | | 01b - Sentinel HTT | [cal.pg.ml](http://cal.pg.ml/) | Calculated mean pg/mL concentration | | 01b - Sentinel HTT | Tissue | corresponding tissue measured | | 01b - Sentinel HTT | normalized | pg/mL normalized to the control geno (fl/fl) in each age and tissue | | 01c - Interim HTT | Tissue | corresponding tissue measured | | 01c - Interim HTT | ID | Individual Mouse Identification number | | 01c - Interim HTT | Run | Individual run of MSD test | | 01c - Interim HTT | Genotype | Mouse genotype | | 01c - Interim HTT | DOB | Date of birth | | 01c - Interim HTT | Sex | Animal sex; Male or Female | | 01c - Interim HTT | Sac.month | age at tissue collection | | 01c - Interim HTT | mean.pg.ml | Calculated mean pg/mL concentration | | 01c - Interim HTT | Mean.Normalized | pg/mL normalized to the control geno (fl/fl) in each age and tissue | | 01c - Interim HTT | AVERAGE.mean.norm | pg/mL normalized to the control geno (fl/fl) in each age and tissue, excluding Run 2 | | 02 - Long. NfL | Mouse | Individual Mouse Identification number | | 02 - Long. NfL | pg.ml.mean | Calculated pg/mL concentration | | 02 - Long. NfL | Month | Age, in months, at tissue collection | | 02 - Long. NfL | Genotype | Mouse genotype | | 02 - Long. NfL | Treatment | Treatment; Vehicle or Tamoxifen | | 02 - Long. NfL | Normalized | pg/mL normalized to the control geno (fl/fl) in each age and tissue | | 03 - Balance beam | Mouse\_id | Individual Mouse Identification number | | 03 - Balance beam | Genotype | Mouse genotype | | 03 - Balance beam | Treatment | Treatment; Vehicle or Tamoxifen | | 03 - Balance beam | Sex | Animal sex; Male or Female | | 03 - Balance beam | Weight | Body weight (grams) | | 03 - Balance beam | Trial\_1 | Balance beam trial 1 | | 03 - Balance beam | Trial\_2 | Balance beam trial 2 | | 03 - Balance beam | Trial\_3 | Balance beam trial 3 | | 03 - Balance beam | Trial\_avg | Average of 3 trials | | 03 - Balance beam | Pokes\_trial | Number of pokes by observer per trial | | 03 - Open field | Test | Testing order for all mice | | 03 - Open field | Group | Testing group  | | 03 - Open field | Mouse\_id | Individual Mouse Identification number | | 03 - Open field | Genotype | Mouse genotype | | 03 - Open field | Treatment | Treatment; Vehicle or Tamoxifen | | 03 - Open field | Sex | Animal sex; Male or Female | | 03 - Open field | Weight | Body weight (grams) | | 03 - Open field | Apparatus | Open field apparatus used for each mouse | | 03 - Open field | entries\_edge | Number of entries into the edge zone | | 03 - Open field | exits\_edge | Number of exits from the edge zone | | 03 - Open field | time\_edge | Time spent in the edge zone (seconds) | | 03 - Open field | distance\_edge | Distance traveled in the edge zone (meters) | | 03 - Open field | first\_exit\_latency\_edge | Time until the first exit from the edge zone (seconds) | | 03 - Open field | average\_speed\_edge | Average speed in the edge zone (meters/hour) | | 03 - Open field | entries\_center | Number of entires into the center zone | | 03 - Open field | exits\_center | Number of exits from the center zone | | 03 - Open field | time\_center | Time spent in the center zone (seconds) | | 03 - Open field | distance\_center | Distance traveled in the center  zone (meters) | | 03 - Open field | first\_exit\_latency\_center | Time until the first exit from the center zone (seconds) | | 03 - Open field | average\_speed\_center | Average speed in the center zone (meters/hour) | | 03 - Open field | ratio | Ratio of time in center to time in edge | | 03 - Open field | distance\_total | Total distance traveled (meters) | | 03 - SHIRPA | Mouse number | Individual Mouse Identification number | | 03 - SHIRPA | Genotype | Mouse genotype | | 03 - SHIRPA | Treatment | Treatment; Vehicle or Tamoxifen | | 03 - SHIRPA | Sex | Animal sex; Male or Female | | 03 - SHIRPA | Measure | SHIRPA measure | | 03 - SHIRPA | 3 | Age (months) | | 03 - SHIRPA | 4 | Age (months) | | 03 - SHIRPA | 5 | Age (months) | | 03 - SHIRPA | 6 | Age (months) | | 03 - SHIRPA | 7 | Age (months) | | 03 - SHIRPA | 8 | Age (months) | | 03 - SHIRPA | 9 | Age (months) | | 03 - SHIRPA | 10 | Age (months) | | 03 - SHIRPA | 11 | Age (months) | | 03 - SHIRPA | 12 | Age (months) | | 03 - SHIRPA | 13 | Age (months) | | 04a - Endpt HTT | Order | Sample order on plate | | 04a - Endpt HTT | calc.conc.mean | Calculated mean pg/mL concentration | | 04a - Endpt HTT | Batch | Individual run of MSD test | | 04a - Endpt HTT | Mouse.Number | Individual Mouse Identification number | | 04a - Endpt HTT | Genotype | Mouse genotype | | 04a - Endpt HTT | Sex | Animal sex; Male or Female | | 04a - Endpt HTT | Treatment | Treatment; Vehicle or Tamoxifen | | 04a - Endpt HTT | Normalized | pg/mL normalized to the control geno (fl/fl) in each age and tissue | | 04a - Endpt HTT | Tissue | corresponding tissue measured | | 04b - Endpt NfL | ID | Individual Mouse Identification number | | 04b - Endpt NfL | Sample | Plate sample ID | | 04b - Endpt NfL | Mean | Variability of technical replicates per mouse | | 04b - Endpt NfL | calc.conc.mean | Calculated mean pg/mL concentration | | 04b - Endpt NfL | Genotype | Mouse genotype | | 04b - Endpt NfL | Sex | Animal sex; Male or Female | | 04b - Endpt NfL | Treatment | Treatment; Vehicle or Tamoxifen | | 04b - Endpt NfL | Group | Individual run of MSD test | | 04b - Endpt NfL | Norm.save | pg/mL normalized to the control geno (fl/fl) in each age and tissue | | 04b - Endpt NfL | Medium | Medium measure; cerebrospinal fluid (CSF), plasma | | 05 - Weights | Mouse.Number | Individual Mouse Identification number | | 05 - Weights | Genotype | Mouse genotype | | 05 - Weights | Sex | Animal sex; Male or Female | | 05 - Weights | Treatment | Treatment; Vehicle or Tamoxifen | | 05 - Weights | Weight.Body | Body weight (grams) | | 05 - Weights | Weight.Brain | Brain weight (grams) | | 05 - Weights | Weight.Liver | Liver weight (grams) | | 05 - Weights | Weight.Spleen | Spleen weight (grams) | | 05 - Weights | Weight.Kidney | Kidney weight (grams) | | 05 - Weights | Weight.Testes | Testes weight (grams) | | 06a - EM | Mouse | Individual Mouse Identification number | | 06a - EM | Target | Target of x-ray; Deposit or tissue | | 06a - EM | cps.eV | Electron volt normalized to count per second | | 06a - EM | keV | Kiloelectron volt | | 06a - EM | Mouse.ID | Individual Mouse Identification number | | 06a - EM | Genotype | Mouse genotype | | 06a - EM | Treatment | Treatment; Vehicle or Tamoxifen | | 06a - EM | Group | Group; control or conditional knockout (cKO) | | 06c - TFRC | Mouse | Individual Mouse Identification number | | 06c - TFRC | Blot | Identification of the specific blot | | 06c - TFRC | TPS\_signal | Total protein signal (TPS) | | 06c - TFRC | TPS\_norm | Total protein signal normalized to fl/fl mice | | 06c - TFRC | Target\_signal | Target (TFRC) signal | | 06c - TFRC | Target\_norm | Target (TFRC) signal normalized to fl/fl mice | | 06c - TFRC | Norm\_btw\_blots | Blot normalized signal | | 06c - TFRC | Mouse\_Number | Individual Mouse Identification number | | 06c - TFRC | Genotype | Mouse genotype | | 06c - TFRC | Sex | Animal sex; Male or Female | | 06c - TFRC | Treatment | Treatment; Vehicle or Tamoxifen | | 07 - IHC | Leroy slide number | Slide number for identification  | | 07 - IHC | Mouse Number | Individual Mouse Identification number | | 07 - IHC | Section | Section type (sagittal or coronal) | | 07 - IHC | Genotype | Mouse genotype | | 07 - IHC | Sex | Animal sex; Male or Female | | 07 - IHC | Treatment | Treatment; Vehicle or Tamoxifen | | 07 - IHC | cKO | Boolean; cKO, true or false | | 07 - IHC | Label | Slide label | | 07 - IHC | Type | Quantification type | | 07 - IHC | Stain | Protein stain (GFAP or IBA1) | | 07 - IHC | Area | Area of thresholded space | | 07 - IHC | Mean | Mean siganal intensity | | 07 - IHC | %Area | Percent of area with signal | | 07 - IHC | Total\_area | Total image area | | 07 - IHC | Adjusted\_total | Final image area with background subtracted | | 07 - IHC | Adjusted\_% | Final signal measure using adjusted area | | 07 - IHC | MinThr | Minimum threshold value for signal measure | | 07 - IHC | MaxThr | Maximum threshold value for signal measure | | S1 - sqPCR interim | Mouse | Individual Mouse Identification number | | S1 - sqPCR interim | Genotype | Mouse genotype | | S1 - sqPCR interim | Month | Age, months | | S1 - sqPCR interim | RecTS | Recombination total signal | | S1 - sqPCR interim | fl/fl.ave | Average control signal | | S1 - sqPCR interim | Normalized | Recombination signal normalized to control signal | | S1 - sqPCR interim | Tissue | corresponding tissue measured | | S1 - sqPCR sentinel | Mouse | Individual Mouse Identification number | | S1 - sqPCR sentinel | Genotype | Mouse genotype | | S1 - sqPCR sentinel | Age.Rounded | Age, in months, rounded to nearest whole number | | S1 - sqPCR sentinel | variable | Measured variable; recombination total signal (RecTS) | | S1 - sqPCR sentinel | value | Value of measured variable | | S1 - sqPCR sentinel | fl.ave | Average control signal | | S1 - sqPCR sentinel | Normalized | Recombination signal normalized to control signal | | S1 - sqPCR sentinel | Tissue | corresponding tissue measured | | S2 - Tissue survey | Number | Sample order on plate | | S2 - Tissue survey | Tissue | corresponding tissue measured | | S2 - Tissue survey | Assay | Protein measured; Huntingtin HTT | | S2 - Tissue survey | Calc.conc.mean | Calculated mean pg/mL concentration | | S2 - Tissue survey | [Calc.conc.CV](http://calc.conc.cv/) | Variability of technical replicates per mouse | | S2 - Tissue survey | Mouse number | Individual Mouse Identification number | | S2 - Tissue survey | Geno | Mouse genotype | | S2 - Tissue survey | Sex | Animal sex; Male or Female | | S3 - plasma chem | Mouse | Individual Mouse Identification number | | S3 - plasma chem | Genotype | Mouse genotype | | S3 - plasma chem | Sex | Animal sex; Male or Female | | S3 - plasma chem | Treatment | Treatment; Vehicle or Tamoxifen | | S3 - plasma chem | Albumin | Measured analyte; Albumin | | S3 - plasma chem | Albumin:GlobulinRatio | Measured analyte; Albumin:GlobulinRatio | | S3 - plasma chem | ALT | Measured analyte; ALT | | S3 - plasma chem | AST | Measured analyte; AST | | S3 - plasma chem | Bilirubin-Total | Measured analyte; Bilirubin-Total | | S3 - plasma chem | BUN | Measured analyte; BUN | | S3 - plasma chem | CO2 | Measured analyte; CO2 | | S3 - plasma chem | CreatineKise(CK) | Measured analyte; CreatineKise(CK) | | S3 - plasma chem | Glucose | Measured analyte; Glucose | | S3 - plasma chem | Phosphorus | Measured analyte; Phosphorus | | S3 - plasma chem | Cholesterol | Measured analyte; Cholesterol | | S7 - Cereb IHC | Pct.Area | Measured analyte; Pct.Area | | S7 - Cereb IHC | Mouse Number | Individual Mouse Identification number | | S7 - Cereb IHC | Genotype | Mouse genotype | | S7 - Cereb IHC | Sex | Animal sex; Male or Female | | S7 - Cereb IHC | Treatment | Treatment; Vehicle or Tamoxifen | | S7 - Cereb IHC | Stain | Immunostain; GFAP or IBA1 | ### Usage notes R is required to open all .R scripts. Scripts were generated using R 4.2.3. Microsoft Excel can be used to view *cKO manuscript rProject source data.xlsx*