Data from: From circuits to lifespan: Translating mouse and human timelines with neuroimaging based tractography
Data files
Mar 06, 2025 version files 3.59 GB
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Gene_data_GSE47966.txt
3.25 MB
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P12_S16_dm.zip
138.48 MB
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P12_S16.zip
131.25 MB
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P12_S17_dm.zip
171.68 MB
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P12_S17.zip
186.80 MB
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P12_S22_dm.zip
168.99 MB
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P12_S22.zip
38.56 MB
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P12_S23_dm.zip
199.15 MB
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P12_S23.zip
43.31 MB
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P21_C1_dm.zip
215.43 MB
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P21_C3_dm.zip
189.18 MB
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P21_C4_dm.zip
209.44 MB
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P21_C6_dm.zip
191.10 MB
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P3_S4_dm.zip
118.91 MB
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P3_S5_dm.zip
125.19 MB
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P3_S5.zip
15.78 MB
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P3_S6.zip
20.29 MB
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P4_S11_dm.zip
142.19 MB
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P4_S11.zip
142.44 MB
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P4_S12_dm.zip
137.64 MB
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P4_S12.zip
145.75 MB
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P60_Em10_dm.zip
211.83 MB
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P60_Em7_dm.zip
207.67 MB
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P60_Em8_dm.zip
234.47 MB
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P60_Em9_dm.zip
205.48 MB
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plateaus_gene_expression1.R
2.20 KB
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README.md
7.07 KB
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Table_1.xlsx
41.10 KB
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Translating_time_Pub_ready_2_4_25.R
15.24 KB
Abstract
This repository contains data and scripts to translate ages across some species as well as neuroimaging scans. The dataset also contains diffusion MR tractography of post-mortem mouse brains, which includes tractography and diffusion metrics. This work builds on our Translating Time resource, which is a tool that equates corresponding ages during development. We collected 1,125 observations from age-related changes in body, bone, dental, and brain processes to equate corresponding ages across humans, mice, and rats. We also acquired high-resolution diffusion MR scans of mouse brains (n=16) of either sex at sdifferent postnatal ages (postnatal day 3, 4, 12, 21, 60) to track brain circuit maturation (e.g., olfactory association, transcallosal pathways).
https://doi.org/10.5061/dryad.8pk0p2nzt
Description of the data and file structure
Tractography: These files can be opened with trackvis (https://trackvis.org). The files in this dataset are compressed (i.e., zipped).
The tractography files includes mouse brains at different ages. The file includes information about age and ID. P stands for postnatal day followed by the individual’s ID number. Each zipped file contains a .trk file and two nifti files. The file ending with .trk is a tractography file is reconstructed with high angular resolution difffusion (HARDI). Both of these files can be opened with the software program Trackvis, which is a free software program to open and analyze diffusion MR data. Go to the file tab, and click on “open track” to open track files. Click on load image to load the niftii files. The .trk files encode the tractographies of mouse brains and the nifti files encode brain structure information
Tractography data from mouse brains at postnatal day 12: P12_S23.zip, P12_S22.zip, P12_S17.zip, P12_S16.zip
Tractography data scans from mouse brains at postnatal day 4: P4_S12.zip, P4_S11.zip
Tractography data scans from mouse brains at postnatal day 3: P3_S6.zip, P3_S5.zip
Diffusion MR metrics: We include diffusion MR metrics from post-mortem mouse brains, which are generated with DSI studio. Some of these are compressed (.gz files). More information about DSI studio is available here: https://dsi-studio.labsolver.org/doc/gui_t2.html
Diffusion MR scans from mouse brains at postnatal day 3: P3_S5_dm.zip, P3_S4_dm.zip
Diffusion MR scans from mouse brains at postnatal day 4: P4_S11_dm.zip, P4_S12_dm.zip
Diffusion MR scans from mouse brains at postnatal day 12: P12_S23_dm.zip, P12_S22_dm.zip, P12_S17_dm.zip, P12_S16_dm.zip
Diffusion MR scans from mouse brains at postnatal day 21: P21_C4_dm.zip, P21_C3_dm.zip, P21_C1_dm.zip, P21_C6_dm.zip
Diffusion MR scans from mouse brains at postnatal day 60: P60_Em10_dm.zip, P60_Em9_dm.zip, P60_Em8_dm.zip, P60_Em7_dm.zip
The .src file is used to generate the .fib file. The source file stores the diffusion weighted images and b-table that can be used to do reconstruction.
The .fib file stores the vector field (fiber orientations) and anisotropy information (the magnitude) that can be used by DSI Studio to conduct fiber tracking. These also contain values used to calculate diffusivity metrics.
The .nii file is a 3D stack of images that stores binary information. The files in this folder are the regions of interest (ROI) used in this study. These ROIs span the cortical white matter. These nifti files need to be overlaid on the fib file to quantify diffusion metrics with DSI studio.
Age alignments: include data and scripts used to generate cross-species age alignments.
Table_1.xlsx is the dataset that contains time points in humans, mice, and rats. These data are expressed in days post-conception and are used to equate corresponding ages across these species. Events are time points. These time points are classified as belonging to life history, locomotion, brain, and bone. A value o1 means they belong to that classification whereas a value of 0 means that the time point does not belong to that category. Each time point is associated with a reference, which is where the data are from.
Translating_time_Pub_ready_2_4_25.R: The R script uses data in Table_1.xlsx to equate ages across species. The script explains the process of generating age alignments from these data.
Transcriptional analysis include the dataset (called Gene_data.txt) and an R script (ending with file extension.R). The data and script are used to extract time points used to generate cross-species age alignments
Gene_data_GSE47966.txt: Dataset that contains normalized gene expression from two humans and mice.
plateaus_gene_expression1.R: This script uses the dataset (Gene_data_GSE47966.txt) to translate ages across species
Files and variables
File: Translating_time_Pub_ready_2_4_25.R
Description: The R script uses Table_1.xlsx to equate ages across humans, mice, and rats. The script explains the process of generating age alignments from these data.
File: Table_1.xlsx
Description: Table1.xlsx is the dataset that contains time points in humans, mice, and rats. These data are expressed in days post-conception and are used to equate corresponding ages across these species. Events are time points. These time points are classified as belonging to Life history, Locomotion, Brain, and Bone. A value o1 means they belong to that classification whereas a value of 0 means that the time point does not belong to that category. Each time point is associated with a reference, which is where the data are from.
Missing data code: NA
File: plateaus_gene_expression1.R
Description: This script uses the data to translate ages across species. This script provides additional information about Gene_data_GSE47966.txt
File: Gene_data_GSE47966.txt
Description: Dataset that contains normalized gene expression across multiple individual mice and humans.
Variables
- num: number
- gene_id: Gene identifier.
- FPKM.x.x: normalized gene expression of a given individual
- FPKM.y.x: normalized gene expression of a given individual
- FPKM.x.1.x: normalized gene expression of a given individual
- FPKM.y.1.x: normalized gene expression of a given individual
- FPKM.x.2.x: normalized gene expression of a given individual
- FPKM.y.2.x: normalized gene expression of a given individual
- FPKM.x.3: normalized gene expression of a given individual
- FPKM.y.3: normalized gene expression of a given individual
- FPKM.x.4: normalized gene expression of a given individual
- FPKM.y.4: normalized gene expression of a given individual
- FPKM.x.5: normalized gene expression of a given individual
- FPKM.y.5: normalized gene expression of a given individual
- FPKM.x.6: normalized gene expression of a given individual
- FPKM.y.6: normalized gene expression of a given individual
- FPKM.x.7: normalized gene expression of a given individual
- FPKM.y.7: normalized gene expression of a given individual
- FPKM.x: normalized gene expression of a given individual
- mean.x: mean normalized gene expression
- FPKM.x.y: normalized gene expression of a given individual
- FPKM.y.y: normalized gene expression of a given individual
- FPKM.x.1.y: normalized gene expression of a given individual
- FPKM.y.1.y: normalized gene expression of a given individual
- FPKM.x.2.y: normalized gene expression of a given individual
- FPKM.y.2.y: normalized gene expression of a given individual
- FPKM.y: normalized gene expression of a given individual
- mean.y: mean normalized gene expression
We used multiple programs to extract data out of the attached data. We used DSI Studio software (https://dsi-studio.labsolver.org/) to quantify several diffusivity metrics (e.g., fractional anisotropy). We also studied diffusion MR tractography. These tractography files can be opened with Trackvis, which is a free software program to open and analyze diffusion MR data. Go to the file tab, and click on "open track" to open track files. Click on load image to load the niftii files.
We also collected time points to generate age alignments across humans and rodents. The scripts and data for these age alignments can be opened with the programming language R. Please see the readme file for more details and Cottam et al., 2025 for more details.
Reference:
Cottam NC, Ofori K, Stoll KT, Bryant M, Rogge JR, Hekmatyar K, Sun J, Charvet CJ. 2025. From circuits to lifespan: translating mouse and human timelines with neuroimaging based tractography. J Neurosci. In Press. doi: 10.1523/JNEUROSCI.1429-24.2025. Epub ahead of print. PMID: 39870528.