-------------------- GENERAL INFORMATION -------------------- This readme file was generated on [2025-03-24] by [Daniil Berezhnoi]. Title of Dataset: Description of Dataset: Principal Investigator: Hong-Yuan Chu, hc948@georgetown.edu, ORCID: 0000-0003-0923-683X. Date of Data Collection: 2021-06-01 to 2024-01-20 Software Dependencies: Python, DEEPLABCUT, MoSeq, GraphPad Prism, Excel and Image J. ------------- FILE OVERVIEW ------------- Directory of Files: Raw datasets, Figure source data. -Raw datasets --6OHDA_experiment Video-tracking data (Figure 1) --mitoPark_experiment Video-tracking data (Figure 2) --LDOPA_experiment Video-tracking data (Figure 4) --6OHDA TH data (Figure 1A) --mitoPark TH data (Figure 2A) -Figure source data --6OHDA_data (Figure 1) --mitoPark_data (Figure 2_3) --LDOPA_data (Figure 4) Relationship Between Files: Figure source data is used to make figures in GraphPad or other software using the tidy data format. Raw datasets (video-tracking) are used to perform analysis using DEEPLABCUT and MoSeq pipelines, while microscopy images (TH data) are used for representative images and quantification of dopamine decline. File Formats: Figure source data contains the data in Microsoft Excel Worksheet in a tidy data format (.xlsx) and GraphPad prism formats (.prism). Raw datasets (TH data) contain microscopy images (.nd2), Microsoft Excel Worksheets (.xlsx), GraphPad prism files (.prism,.pzfx) and representative pictures in (.ai, .pptx) format. File Naming Convention: Based on file formats. ---------------------------------------- DATA SPECIFIC INFORMATION FOR [Figure source data] Date of Creation: 2025-03-24 Description of Data: Source data is used to make figures in GraphPad. A. Missing data are represented as empty cells. DATA SPECIFIC INFORMATION FOR [Raw datasets TH data] Date of Creation: 2025-03-24 Description of Data: Microscopy images are used to make representative images A. Raw pictures are contained in the Histological slides subfolder and named using animal ID (for mitoPark TH data) B. Summary tables used for calculation of the mean values are included as Microsoft Excel Worksheets (.xlsx), GraphPad prism files (.prism,.pzfx) C. Final representative pictures are saved in Illustrator (.ai) and Powerpoint (.pptx) files ------------- METADATA FOR [Raw datasets TH data] ------------- Metadata is created according to The Brain Image Library metadata schema. Schema can be found at https://www.google.com/url?q=https://www.brainimagelibrary.org/newmetadatamodel.html&source=gmail-imap&ust=1750454863000000&usg=AOvVaw0EV7zeTYtYpR8jFSCVm0qz Contributors ------------- contributorName: Liqiang Chen, Chu lab Creator: Liqiang Chen contributorType: Researcher nameType: Personal nameIdentifier: ORCID 0000-0003-3236-1129 (Liqiang Chen) nameIdentifierScheme: ORCID affiliation: Georgetown University affiliationIdentifier: https://www.google.com/url?q=https://orcid.org/members/001G000001iVrmIIAS&source=gmail-imap&ust=1750454863000000&usg=AOvVaw1N8BnyvCAi5divdQGURQCy affiliationIdentifierScheme: ORCID Dataset ------------- Title: Tyrosine-hydroxylase hitochemistry for mitoPark mice Rights: CC-BY 4.0 rightsIdentifier: https://www.google.com/url?q=https://spdx.org/licenses/CC-BY-4.0.html&source=gmail-imap&ust=1750454863000000&usg=AOvVaw2ISdPj5H0GyIsY2T8PNIfn Abstract: Immunohistochemical staining of the mouse striatum for TH created to verify the extension of DA neurodegeneration in mitoPark mice Instrument ------------- Microscope: confocal laser scanning microscope MicroscopeManufacturerAndModel: Nikon A1R Image ------------- xAxis: Right to left yAxis: Superior to inferior zAxis: Anterior to posterior displayColor: RGB Specimen ------------- Species: mouse NCBITaxonomy: Mus musculus (10090) Age: 24 Ageunit: weeks Sex: Male, Female DATA SPECIFIC INFORMATION FOR [Raw datasets Video-tracking data] Date of Creation: 2025-03-24 Description of Data: Raw videos used for video-tracking of animal posture and analysis using MoSeq pipeline A. Raw videos are included in MP4 file format and images are named based on time of the recording and animal ID B. Each folder contains the 'file_index.csv' file showing the names of the files with animal IDs and experimental groups C. Tracking data from the DEEPLABCUT package used in the MoSeq analysis for each video is contained in the 'tracking_data' subfolder with the same names as videos ----------- METHODOLOGY ----------- Description of methods used for data collection: Video data for 6OHDA and mitoPark groups is collected using the Microsoft Kinect depth video camera with the framerate of 30fps. Video dat for LDOPA experiment is collected using FLIR Blackfly S camera with the framerate of 50fps and then downsampled to 25fps. Microscopy images are collected using a confocal microscope. Description of methods used for data processing: A. Video data is processed using the custom software pipelines - DeepLabCut (Mathis et al., 2019) to acquire 7-point tracking of the animal posture (step 1) B. Animal posture data is fed into Keypoint-MoSeq pipeline (Weinreb et al., 2024) for Markov Chain modeling of animal motion sequences. B. Microscopy images are processed using Image J software to quantify the TH staining. C. All data after processed through Python pipelines and Image J is put into GraphPad to make figures. ----------------------- DATA ACCESS AND SHARING ----------------------- This research was funded in part by Aligning Science Across Parkinson’s (ASAP-020572) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF).