A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types
Data files
Sep 19, 2023 version files 96.71 MB
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GF_TE_sc_data_2023.zip
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GF_TE_st_data_2023.zip
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README.md
Sep 26, 2023 version files 96.71 MB
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GF_TE_sc_data_2023.zip
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GF_TE_st_data_2023.zip
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README.md
Abstract
Teleost fish form the largest group of vertebrates, making them critically important for the study on the mechanisms of brain evolution. In fact, teleosts show a tremendous variety of adaptive behaviors similar to birds and mammals, however, the neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon: the seat of plastic behavior, learning, and memory in vertebrates. We delineated and mapped goldfish telencephalon cell types using single-cell RNA-seq and spatial transcriptomics, resulting in de novo molecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin (SST) interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus, but molecularly conserved. Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly conserved goldfish homologs. We further suggest different elements of a hippocampal formation across the goldfish pallium. Finally, aiding study of the teleostan everted telencephalon, we describe substantial molecular similarities between the goldfish and zebrafish neuronal taxonomies. Together, our atlas provides new insights into organization and evolution of vertebrate forebrains and may serve as a resource for the functional study underlying cognition in teleost fish.
README: Upload Files
This repository contains the data and code associated with the scientific article titled "A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types". The research employed various techniques, including single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics, to elucidate the molecular neuroanatomy and evolutionary aspects of the goldfish telencephalon.
The following dataset files are available
Dryad (Data)
- GF_TE_sc_data_2023.zip - Single-cell datasets for the goldfish telencephalon used in the article. This archive includes the following files:
sc_data.csv
- Single-cell count matrix (genes- rows\, cells- columns).genes.csv
- Genes list.cell_type_name.csv
- Cell type names list.sample_region.csv
- Table of flags indicating single cell (rows) with sample number\, region (columns).
- GF_TE_st_data_2023.zip - Spatial transcriptomics datasets for the goldfish telencephalon used in the article. This archive includes the following files:
data.csv
- Spatial transcriptomics count matrix (genes- rows\, spots- columns).geneid.csv
- Genes list.mapped_xy_all.csv
- Spatial location barcodes for Visium spot samples ( column 1 - X column 2- Y\, rows- spots).samples.csv
- Flags indicating sample for each spot.barcodes.csv
- barcode ID for each spot in each sample.
Zenodo (Software)
The following dataset files are available in the Zenodo directory:
- GF_TE_sc_p1.zip - Attached codes (part 1) for first layer single-cell analysis (e.g. QC\, preprocessing\, normalization clustering\, and embedding) used in the article.
- GF_TE_sc_p2.zip - Attached codes (part 2) for advanced various analyses\, including spatial transcriptomics\, comparative data integration\, and single-cell to spatial deconvolution. These are organized to maintain a logical flow in the code.
Supplemental information:
- SupplTable_HCR-probes.xlsx - An Excel spreadsheet providing a table of customized HCR (Hybridization Chain Reaction) gene probes used in the study. It contains information about genes and their corresponding probe sequences.
- GABA_spatial_all_FISH1_2.pdf- High-resolution spatial mapping for scRNAseq GABAergic cell types of goldfish to spatial transcriptomic Visium slide spots.
- GLUT_spatial_all_FISH1_2.pdf- High-resolution spatial mapping for scRNAseq Glutamatergic cell types of goldfish to spatial transcriptomic Visium slide spots.
Sharing/Access Information
The data and code in this repository are accessible directly through this repository. To access the data files, simply download the respective zip files mentioned above. The files are provided in a compressed format to facilitate easier and faster downloads.
If you have any further questions or need assistance with specific files or issues, please don't hesitate to contact the authors of the article or the repository maintainers for additional guidance. [muhammadtibi@campus.technion.ac.il]
Code/Software
The code files provided in the "GF_TE_sc_p1.zip" and "GF_TE_sc_p2.zip" folders are written in MATLAB programming language. The code utilizes various libraries and packages for data analysis and visualization.
It is recommended to use the following software versions and add-on packages(or compatible ones) to run the codes:
[MATLAB Version 9.11 (R2021b)
Bioinformatics Toolbox Version 4.15.2 (R2021b)
Communications Toolbox Version 7.6 (R2021b)
Computer Vision Toolbox Version 10.1 (R2021b)
Curve Fitting Toolbox Version 3.6 (R2021b)
DSP System Toolbox Version 9.13 (R2021b)
Database Toolbox Version 10.2 (R2021b)
Deep Learning HDL Toolbox Version 1.2 (R2021b)
Deep Learning Toolbox Version 14.3 (R2021b)
Econometrics Toolbox Version 5.7 (R2021b)
Embedded Coder Version 7.7 (R2021b)
GPU Coder Version 2.2 (R2021b)
Global Optimization Toolbox Version 4.6 (R2021b)
Image Processing Toolbox Version 11.4 (R2021b)
MATLAB Coder Version 5.3 (R2021b)
Mapping Toolbox Version 5.2 (R2021b)
Optimization Toolbox Version 9.2 (R2021b)
Parallel Computing Toolbox Version 7.5 (R2021b)
R Connectivity Tools Version 1.0 (R14)
Reinforcement Learning Toolbox Version 2.1 (R2021b)
Robotics System Toolbox Version 3.4 (R2021b)
Signal Processing Toolbox Version 8.7 (R2021b)
Statistics and Machine Learning Toolbox Version 12.2 (R2021b)
Symbolic Math Toolbox Version 9.0 (R2021b)
Tensor Toolbox (Sandia National Labs) Version 3.1
Vision HDL Toolbox Version 2.4]
Please refer to the individual code files for specific instructions on running the code and any additional dependencies.
Feel free to explore, use, and modify these MATLAB files according to your needs. instructions and usage guidelines are provided within each file. If you encounter any issues or have suggestions for improvement, please feel free to open an issue or submit a pull request.
License
Software Files (Zenodo)
The software files included in this repository, including source code, scripts, and documentation, are licensed under the MIT License.
Data (Dryad)
The data associated with this project, which is hosted on Dryad, is made available under the CC0 license waiver.
Acknowledgments
If you use these MATLAB files in your research or project, please consider citing this repository or providing acknowledgment. Contact For additional data and subfunctions that can be provided by specific request, and if you have any questions or inquiries regarding this repository, please contact us by email at [muhammadtibi@campus.technion.ac.il] or [stavbi@post.bgu.ac.il].