.. _Data sources: 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 :ref:`Browse database` tab or by following the respective DOI. For information on the licenses of the datasets look here: `Licences data `_. .. _Mouse 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: 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 a. **Song_2020_Nowakowski_2017**: Transcriptomes of single cells from the developing brain (**frontal cortex**), DOI: 10.1126/science.aap8809 b. **Song_2020_Darmanis_2015**: A survey of human **cortical transcriptome** diversity at the single cell level, DOI: 10.1073/pnas.1507125112 c. **Song_2020_Zhong_2018**: A single-cell RNA-seq survey of the developmental landscape of the human **prefrontal cortex**, DOI: 10.1038/nature25980 d. **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 e. **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 f. **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 g. **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 h. **Song_2020_La_Manno_2016**: Single-cell RNA sequencing of human embryonic **ventral midbrain** i. **Song_2020_Habib_2017**: Massively parallel single-nucleus RNA-seq with DroNc-seq of **hippocampal gyrus and frontal lobe**, DOI: 10.1038/nmeth.4407 j. **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 ``_ )