Data in BrainTrawler

In BrainTrawler, we have integrated a collection of public neuroscience datasets of Brain Transcriptomic And Connectivity Data (BrainTACO) for mouse and human. For most gene expression data resources, single-cell RNA sequencing was used. This page gives you an overview of the availble sources. More information on the datasets can be found using either the Browse Database tab or by following the respective DOI. For information on the licenses of the datasets look here: Licences data.

Mouse data

RNA sequencing data

  1. Gokce_2016: Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq, DOI: 10.1016/j.celrep.2016.06.059

  2. Bhattacherjee_2019: Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction, DOI: 10.1038/s41467-019-12054-3

  3. Yao_2021: Single-cell transcriptomes from multiple cortical areas and the hippocampal formation of 8 week old pan-GABAergic, pan-glutamatergic, and pan-neuronal transgenic lines, with the addition of more specific transgenic lines and some retrogradely-labeled cells in VISp and ALM, DOI: 10.1101/2020.03.30.015214

  4. Campbell_2017: A molecular census of arcuate hypothalamus and median eminence cell types, DOI: 10.1038/nn.4495

  5. Rossi_2019: Single-cell RNA sequencing of of the lateral hypothalamic area, DOI: 10.1126/science.aax1184

  6. Gouwens_2020: Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. In addition to transcriptomic celltypes, morpho-electric (ME) celltypes are matched to the transcriptomic celltypes. DOI: 10.1101/2020.02.03.932244

  7. Zeisel_2018: Atlas of celltypes from the Linnarsson Lab as available at mousebrain.org, DOI: 10.1016/j.cell.2018.06.021

  8. Lein_2007: A genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain. In situ hybridization image data with cellular-level resolution, DOI: 10.1038/nature05453

Network data

  1. Allen_Brain_Axonal_Projections: Axonal projections of 2173 injections sites labeled by rAAV tracers and visualized using serial two-photon tomography (connectivity.brain-map.org). Data has been mirrored to be available on both hemispheres, resulting in a total of 4346 injection sites, DOI: 10.1038/nature13186

Human data

RNA sequencing data

  1. Hawrylycz_2012: Microarray data providing an all genes, all structures survey in multiple adult control brains. DOI: 0.1038/nature11405

  2. BrainSpan_2013: Bulk RNA-Sequencing data for studying transcriptional mechanisms involved in human brain development. Samples are split between adult (older than or equal 19 years) and non adults (younger than 19 years). This information is encoded in the celltype information, www.brainspan.org

  3. Lee_2020: Cell Type-Specific Transcriptomics. Data filtered for control (healthy individuals) and striatum (caudate nucleus and putamen). DOI: 10.1016/j.neuron.2020.06.021

  4. Hodge_2019: Single-nucleus RNA-sequencing of cell types in the middle temporal gyrus of human cortex, DOI: 10.1038/s41586-019-1506-7

  5. Song_2020: Couple of datasets integrated from STAB: a spatio-temporal cell atlas of the human brain, DOI: 10.1093/nar/gkaa762

    1. Song_2020_Nowakowski_2017: Transcriptomes of single cells from the developing brain (frontal cortex), DOI: 10.1126/science.aap8809

    2. Song_2020_Darmanis_2015: A survey of human cortical transcriptome diversity at the single cell level, DOI: 10.1073/pnas.1507125112

    3. Song_2020_Zhong_2018: A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex, DOI: 10.1038/nature25980

    4. Song_2020_Fan_2018: Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis, DOI 10.1038/s41422-018-0053-3

    5. Song_2020_Li_2018_Part1: Single-cell RNA sequencing (scRNA-seq) data generated from 1195 cells collected from embryonic fronto-parietal neocortical wall and mid-fetal fronto-parietal neocortical plate and adjacent subplate zone of an independent set of nine brains ranging in age from 5 to 20 postconceptional weeks, DOI: 10.1126/science.aat7615

    6. Song_2020_Li_2018_Part2: Single-cell RNA sequencing (scRNA-seq) data of the dorsolateral prefrontal cortex generated from three adult brains, DOI: 10.1126/science.aat7615

    7. Song_2020_Lake_2018: Single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq) data from human adult visual cortex, frontal cortex, and cerebellum, DOI: 10.1038/nbt.4038

    8. Song_2020_La_Manno_2016: Single-cell RNA sequencing of human embryonic ventral midbrain

    9. Song_2020_Habib_2017: Massively parallel single-nucleus RNA-seq with DroNc-seq of hippocampal gyrus and frontal lobe, DOI: 10.1038/nmeth.4407

    10. Song_2020_Welch_2019: Single-cell sequencing of the substantia nigra, DOI: 10.1016/j.cell.2019.05.006

Network data

  1. WU-Minn_HCP_RestingState: Resting-state connectivity (WU-Minn HCP Data https://db.humanconnectome.org )