Fast and slow strains of misfolded superoxide dismutase 1 in amyotrophic lateral sclerosis
Data files
May 06, 2026 version files 193.75 GB
-
Figure_1B_G85R-YPF_injected_by_G37R_by_ScN.zip
19.04 GB
-
Figure_2_S4_230_P0_injection.zip
144.10 GB
-
Figure_S2_P0_isc_G85R-YFP_mice.zip
30.61 GB
-
Final_list_Xu_et_al_for_raw_data_uploading.xlsx
73.64 KB
-
README.md
13.85 KB
Abstract
Mutations in superoxide dismutase 1 (SOD1) account for ~10% of familial amyotrophic lateral sclerosis (fALS) cases. Most SOD1 ALS cases show a 2-5 year clinical course, but a subset of patients exhibit a slowly progressing illness lasting 10-20 years. Substantial evidence indicates that disease-causing mutations in SOD1 promote misfolding and aggregation. Spinal tissue homogenates from paralyzed transgenic mice containing misfolded mutant SOD1 accelerate paralysis when injected into the spine or sciatic nerve of young mutant SOD1 transgenic mice. Using this prion-like seeding model in G85R-SOD1:YFP transgenic mice to initiate the disease process, we show that human SOD1 variants associated with rapidly progressing ALS produce SOD1-ALS strains that cause paralysis earlier than mutations associated with slowly progressing disease. This data set contains image data documenting pathological features of mice that became paralyzed by seeding injections.
Dataset DOI: 10.5061/dryad.s7h44j1mf
Description of the data
This Dryad dataset contains the raw animal information and raw image data used for the study “Fast and slow strains of misfolded superoxide dismutase 1 in amyotrophic lateral sclerosis.” The dataset includes one Excel workbook summarizing all animals used in the study and three compressed (.zip) folders containing raw microscopy and digital slide images organized by figure and experimental group.
All animals used in this study are documented in the Excel file Final_list_Xu_et_al_for_raw_data_uploading.xlsx. This workbook contains 22 tabs. Each tab corresponds to a specific animal dataset used for one or more figures. Animals injected with the same inoculum are grouped on a single sheet. The tab names are organized by figure number and experimental group name; these group names correspond to the labels used on the X-axis in the associated figures.
The image data are stored in three .zip files. After unzipping, each folder is organized primarily by figure number and then by experimental group. The raw images include direct YFP fluorescence images and whole-slide images from stained tissue sections.
File formats and software
.xlsx: Excel workbook containing animal metadata, clinical notes, incubation periods, pathology scores, and figure-use notes..tiff: Direct YFP fluorescence microscopy images..svs: Aperio whole-slide digital scans of Campbell-Switzer silver-stained sections and Ubi-1 immunostained sections.
The .svs files can be viewed with Aperio ImageScope or other compatible whole-slide image viewers. Aperio ImageScope is available from Leica Biosystems: https://www.leicabiosystems.com/us/digital-pathology/manage/aperio-imagescope/
Naming conventions and experimental terms
The following terms are used in the Excel workbook, folder names, and/or image file group names:
- G37R, G85R, G93A, H46R, and N139K: Mutations of SOD1. When one of these mutation names is used as the name of an inoculum, it indicates the initial source mutation of the seed-containing homogenate.
- A4V-3: Homogenate originally generated from an ALS patient carrying the A4V SOD1 mutation. A4V-2 and A4V-3 are internal labels used to distinguish two different A4V patient-derived sources for later inoculum naming.
- 230 / Line 230: A transgenic mouse line expressing G85R-SOD1:YFP with LoxP sites. In this dataset, “230” in an inoculum or folder name indicates inoculum material derived from Line 230 mice.
- Y230: Young Line 230 mice; the spinal cord homogenate pool was prepared from four healthy young mice. In this dataset, Y230 serves as the negative control for the 230 pool, which was prepared from paralyzed mice.
- 230-11: Homogenate generated from one uninoculated paralyzed mouse from Line 230.
- 0.25x and 5x: Relative dilution/concentration of the inoculum compared with the standard inoculum preparation used for the corresponding experiment.
- Asym: Asymptomatic. This indicates that the mouse did not show clinical symptoms at the time relevant to tissue collection.
- E10-83 (A4V-2), JHU74 (A4V-3), and JHU83 (N139K): Patient identifiers from the Emory University Brain Bank or Johns Hopkins Brain Bank. The mutation shown in parentheses indicates the SOD1 mutation present in that patient. The labels A4V-2 and A4V-3 distinguish the two A4V patient-derived sources for internal use in later inoculum naming.
- P1, P2, and P3: Passage number of the inoculum or homogenate.
- pool: A pooled homogenate prepared from multiple animals or source samples within the indicated group.
Dataset file structure
The dataset contains the following files before unzipping:
Dryad_dataset/
├── Final_list_Xu_et_al_for_raw_data_uploading.xlsx
├── Figure_1B_G85R-YPF_injected_by_G37R_by_ScN.zip
├── Figure_2_S4_230_P0_injection.zip
└── Figure_S2_P0_isc_G85R-YFP_mice.zip
After unzipping the three compressed folders, the expected data structure is:
Dryad_dataset/
├── Final_list_Xu_et_al_for_raw_data_uploading.xlsx
│
├── Figure_1B_G85R-YPF_injected_by_G37R_by_ScN/
│ ├── NTg homogenate controls/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ └── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ ├── P1 G37R cohort 1/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ └── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ ├── P1 G37R cohort 2/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ └── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── P1 G37R cohort 3/
│ ├── YFP fluorescence images (*.tiff)
│ └── Campbell-Switzer silver-stained Aperio scans (*.svs)
│
├── Figure_2_S4_230_P0_injection/
│ ├── 230 pool/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── 230 pool 0.25x/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── A4V-3 P2 pool/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── Asym 230 control/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── G37R P3 pool/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── G85R P2 pool/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── G93A P2 pool/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── H46R P2 pool/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ │ └── Ubi-1 immunostained Aperio scans (*.svs)
│ ├── H46R P2 pool 5x/
│ │ ├── YFP fluorescence images (*.tiff)
│ │ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── N139K P2 pool/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
│
└── Figure_S2_P0_isc_G85R-YFP_mice/
├── 5x E10-83 (A4V-2)/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
├── 5x JHU74 (A4V-3)/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
├── 5x JHU83 (N139K)/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
├── G85R-SOD1-YFP (230-11)/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
├── P1-A4V (G85R-SOD1-YFP) A4V-2/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
├── P1-A4V (G85R-SOD1-YFP) A4V-3/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
├── P1-H46R (G85R-SOD1-YFP)/
│ ├── YFP fluorescence images (*.tiff)
│ ├── Campbell-Switzer silver-stained Aperio scans (*.svs)
│ └── Ubi-1 immunostained Aperio scans (*.svs)
└── P1-N139K (G85R-SOD1-YFP)/
├── YFP fluorescence images (*.tiff)
├── Campbell-Switzer silver-stained Aperio scans (*.svs)
└── Ubi-1 immunostained Aperio scans (*.svs)
Note: Some experimental groups may not contain all three image types because that staining or imaging method was not performed for that animal or group. The Excel workbook should be used as the index for determining which animals and images were used for each figure.
Files and variables
File: Final_list_Xu_et_al_for_raw_data_uploading.xlsx
Description: This workbook lists all animals used in the study. Each tab corresponds to one experimental dataset or figure-related animal group.
Column descriptions:
- MouseID: Animal identifier composed of the mouse cage ID assigned by the University of Florida Animal Care Services and the tail tattoo number, usually 1–5 per cage. For example,
1234567-2indicates mouse #2 in cage 1234567. - Sex: Sex of the animal.
- Age: Cumulative age at the time of euthanasia.
- Symptoms: Clinical evaluation notes at the time of euthanasia.
- Incubation: Incubation period, defined as the interval between homogenate injection and appearance of paralysis, reported in months (
mo). - YFP aggregates: Semi-quantitative severity score for direct fluorescence of pathologic inclusions produced by mutant superoxide dismutase 1 (SOD1) fused to yellow fluorescent protein (YFP).
- Silver staining: Semi-quantitative severity score for pathology detected by Campbell-Switzer silver staining.
- Ubi-1: Semi-quantitative severity score for pathology detected by ubiquitin immunostaining using the Ubi-1 antibody.
- Notes: Notes indicating which animals or images were used in specific figures in the accompanying publication, including animals used to generate homogenates for later passages. Cells without notes are filled with a hyphen (
-) to prevent errors when the file is exported or processed as a.csvfile.
For the pathology scoring columns, the relative severity of spinal cord pathologic abnormalities is recorded as -, +, ++, or +++. The abbreviation n.d. indicates that the staining was not done.
File: Figure_1B_G85R-YPF_injected_by_G37R_by_ScN.zip
Description: This compressed folder contains direct YFP fluorescence images (.tiff) and Aperio whole-slide scans (.svs) of Campbell-Switzer silver-stained sections showing aggregates. Four groups of mice were used in this part of the study. Images from two representative animals from this dataset were used to generate Figure S1, where animal IDs were labeled in the bottom-left corner of each image.
Groups included:
- NTg homogenate controls
- P1 G37R cohort 1
- P1 G37R cohort 2
- P1 G37R cohort 3
File: Figure_2_S4_230_P0_injection.zip
Description: This compressed folder contains direct YFP fluorescence images (.tiff) and Aperio whole-slide scans (.svs) of sections stained by Campbell-Switzer silver staining or by Ubi-1 immunohistochemistry. All animals in this dataset were used to generate the survival curves in Figure 2 and Figure S4. Eight representative images from each image set were used to generate Figure 3 and Figure S5.
Groups included:
- 230 pool
- 230 pool 0.25x
- A4V-3 P2 pool
- Asym 230 control
- G37R P3 pool
- G85R P2 pool
- G93A P2 pool
- H46R P2 pool
- H46R P2 pool 5x
- N139K P2 pool
File: Figure_S2_P0_isc_G85R-YFP_mice.zip
Description: This compressed folder contains direct YFP fluorescence images (.tiff) and Aperio whole-slide scans (.svs) of sections stained by Campbell-Switzer silver staining or by Ubi-1 immunohistochemistry. The mice used to make homogenates for the next passage are identified in the workbook notes. All animals in this dataset were used to generate the survival curves in Figure S2, except animals for which tissue was not available.
Groups included:
- 5x E10-83 (A4V-2)
- 5x JHU74 (A4V-3)
- 5x JHU83 (N139K)
- G85R-SOD1-YFP (230-11)
- P1-A4V (G85R-SOD1-YFP) A4V-2
- P1-A4V (G85R-SOD1-YFP) A4V-3
- P1-H46R (G85R-SOD1-YFP)
- P1-N139K (G85R-SOD1-YFP)
Relationship between files
The Excel workbook is the main index for the dataset. The animal IDs, experimental groups, clinical information, pathology scores, and figure-use notes in the workbook should be used to interpret the image folders. The image folders contain the matching raw images for the animals and groups described in the workbook.
Abbreviations
- Asym: Asymptomatic
- ALS: Amyotrophic lateral sclerosis
- CS: Campbell-Switzer silver staining
- NTg: Non-transgenic
- P1, P2, P3: Passage number of inoculum or homogenate
- ScN: Sciatic nerve injection
- SOD1: Superoxide dismutase 1
- Ubi-1: Ubiquitin antibody (made by EnCor Biotechnology Inc. in Gainesville, FL, USA)
- YFP: Yellow fluorescent protein
Tissue Collection
Mice were anesthetized with isoflurane and perfused transcardially with 20 mL of PBS. The spinal column and brain were immediately removed. In some animals, brains were bisected sagittally; one hemisphere was immersion-fixed in 4% paraformaldehyde (PFA) in PBS for 24–48 hours at 4°C, and the other hemisphere flash-frozen on dry ice. Spinal columns were divided into four segments. Cervical and lumbar regions were de-roofed and immersion-fixed, while the remaining segments were flash-frozen. In mice injected in the sciatic nerve, the entire brain and spinal column were immersion-fixed before spinal cord dissection. Mice that were used to produce seeding homogenates were anesthetized and perfused as above, and then the entire spinal cord was removed and frozen. The brain was bisected sagittally with one hemisphere immersion-fixed in 4% paraformaldehyde (PFA) in PBS for 24–48 hours at 4 °C, and the other hemisphere flash-frozen on dry ice. Fixed tissues were paraffin-embedded, and frozen tissues were stored at −80 °C.
Neuropathology and Acquisition of Images
For YFP fluorescence, 5 µm formalin‑fixed paraffin‑embedded (FFPE) sections were deparaffinized, coverslipped with water, and imaged directly using an epifluorescence microscope (Olympus BX60) or a confocal microscope (Nikon Eclipse Ti2). After imaging, coverslips were removed, and sections were either stained by the Campbell-Switzer silver stain as previously described [20,26] or immunostained with antibodies to ubiquitin. For immunohistochemistry, sections were steamed in citrate buffer (pH 6.0) for ~30 min for heat‑induced antigen retrieval. After rinsing in water, sections were blocked with 3% normal goat serum and then incubated overnight at room temperature with the Ubi‑1 primary antibody (1:1000, EnCor Biotechnology, Gainesville, FL, #MCA-Ubi-1). Endogenous peroxidases were quenched with 0.3% H₂O₂ in PBS containing Tween 20 for 10 min. Following additional rinses, sections were incubated with a biotinylated anti‑mouse secondary antibody (1:500), treated with ABC‑HRP, and developed using DAB chromogen. Slides were counterstained with hematoxylin, scanned using an Aperio ScanScope (Leica Biosystems, Deer Park, IL), and processed in GIMP (v3.0.4) for image cropping and scale bar insertion based on pixel calibration with ImageScope. The images deposited here include tiff files and .svs files that are readable with Scan Scope software.