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Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.
Pubmed ID: 34616066 RIS Download
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Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsEncyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome.
View all literature mentionsA software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.
View all literature mentionsAlignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.
View all literature mentionsPortal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.
View all literature mentionsSoftware tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets.
View all literature mentionsCore facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.
View all literature mentionsData repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
View all literature mentionsConsortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.
View all literature mentionsA powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
View all literature mentionsSoftware Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
View all literature mentionsSoftware R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets.
View all literature mentionsSoftware package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting.
View all literature mentionsSoftware R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute.
View all literature mentionsSoftware tool to detect doublets in single-cell RNA-seq data. Software algorithm to remove doublets. Python code for identifying doublets in single-cell RNA-seq data. Framework for predicting impact of multiplets in given analysis and identifying problematic multiplets.
View all literature mentionsHuman and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
View all literature mentionsSoftware tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.
View all literature mentionsSoftware tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.
View all literature mentionsSoftware package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023.
View all literature mentionsBenchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds.
View all literature mentionsLiquid handling instrument designed to optimize dependability and walk-away time. Biomek i7 Hybrid with enclosure has up to 45 deck positions and includes both Multichannel and Span-8 pipette heads in enclosed work space.
View all literature mentionsSemi automated pipetting system by Mettler Toledo. Instrument for semi-automated 96/384-well plate pipetting. Semi-Automated 96/384-Well Pipetting System where pipetting options range from 0.5 uL to 1000 uL.
View all literature mentionsSwinging bucket benchtop centrifuge. Eppendorf 5920 R refrigerated centrifuge.
View all literature mentionsSystem unleashes groundbreaking innovations that leverage our proven technology. Now you can get scalable throughput and flexibility for virtually any sequencing method, genome, and scale of project.
View all literature mentionsFluorescence activated cell sorting instrument by BD Biosciences. Flow cytometer as high speed fixed alignment benchtop cell sorter. Cytometer can be operated at varied pressures and can acquire up to 70,000 events per second. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time.
View all literature mentionsAllen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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