DOI: 10.5061/dryad.qfttdz0p9
title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

description: 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.
description: 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. #
 Upload Files The following dataset files are available ### Dryad (Data) 1.
 **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 \(columns\)\.
 2. **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: 1. **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\. 2. **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].