Mouse brain transcriptome atlas. John Wiley & Sons Inc (2008).
This procedure has been applied to 200 genes in the postnatal mouse brain. The transcripts from these genes make up the mouse transcriptome and are measured by GeoMx MuWTA. Citation: Carson JP, Ju T, Lu H-C, Thaller C, Xu M, Pallas SL, et al. The colorimetric ISH was performed on frozen sagittal sections of C57BL/6J wild-type mice at E14. 1 to ∼76. Scope: Format: Amount: GEO accession: Series GSE222510. The datasets contain a total of ~4 million cells passing rigorous quality-control (QC) criteria. However, our understanding in gene expression Dec 13, 2023 · This study presented a single-cell DNA methylation and 3D multi-omic atlas of the entire mouse brain. The recent integration of Mar 7, 2023 · Jiang et al. Single cell sequencing modalities for neuroscience. 4: Impact of aging on the mouse brain metabolome. 1 across all samples) genes by different gene types. A Digital Atlas for the Mouse Brain Transcriptome Linking expression levels to locations in the atlas From the 24 sections for each gene, we identified the sections that best matched the anatomy represented by standard maps 2, 4, 6, 9 and 11, which collectively are sufficient to characterize all 15 different major anatomical structures in the Dec 8, 2023 · The Allen Mouse Brain Atlas provides genome-wide in situ hybridization (ISH) image data for approximately 20,000 genes in adult mice. A molecular atlas of cell types and zonation in the brain May 24, 2018 · Single-cell transcriptomics reveal novel molecular markers specific to glomerular cell types. present a detailed three-dimensional spatial transcriptome atlas of all major organs in the mouse embryo at E13. A Molecular Atlas of the Adult Mouse Brain. 2: Single-nuclei transcriptome atlas of mouse dorsal root ganglia (DRG) sensory neurons. Here, by combining spatial transcriptomics (scStereo-seq) and scRNA-seq, we built a spatiotemporal developmental atlas of multiple human brain regions from 6-23 gestational weeks (GWs). 1 mm 2), respectively (Figure S1A). Mar 12, 2024 · Nisha Hemandhar Kumar, Verena Kluever, Emanuel Barth, Sebastian Krautwurst, Mattia Furlan, Mattia Pelizzola, Manja Marz, Eugenio F Fornasiero, Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain, Nucleic Acids Research, Volume 52, Issue 6, 12 April 2024, Pages 2865–2885 Oct 30, 2023 · The cellular landscape in the human and mouse brain. tfatlas. These standard sections exhibit the hemi-brain by spanning from lateral (section 1) to paramedial (section 11). Title. Query DataSets for GSE222510. develop a consensus atlas of the human brain transcriptome in Alzheimer’s disease, based on 2,114 postmortem samples, and examine overlap with 251 expression signatures from mouse brain RNA sequencing experiments, including many neurodegenerative disease models. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. Keywords: whole brain, single cell RNA-Seq, transcriptome, mouse: Total Files in Mar 11, 2024 · Nevertheless, the mouse lemur cell atlas included several neuronal subtypes from the brain cortex, brainstem, and retina, as well as both UCP1-high and UCP1-low adipocytes from multiple tissues 15 Oct 15, 2021 · Similar trajectories have been observed in the brain transcriptome map 10, the synapse atlas 4, and brain functional connectivity 43. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain. 2 mm 2) and whole mouse embryos (∼7. Method. They Aug 16, 2023 · A spatiotemporal transcriptome map of the aging mouse brain identifies region-specific acceleration of glial aging, particularly in white matter, distinctive regional responses to rejuvenation interventions, and regional age-associated expression patterns of genes tied to human neurodegenerative diseases. 1 Jan 18, 2011 · The Transcriptome Atlas. A gene atlas of The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. Regional differences in gene expression have been shown to reflect the embryologic imprint (Zapala et al. 3 million cells using MERFISH. Feb 19, 2024 · A spatial molecular atlas of the aging mouse brain is established, which provides important resources and novel insights into the molecular mechanism of brain aging. Fig. They Dec 13, 2023 · Read the paper: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. ECs from brain/testis, liver/spleen, small intestine Dec 1, 2016 · The results show that clustering voxels in the low-dimensional space is more consistent with neuroanatomy than in the original space. BrainTx was developed from the Cerebellar Jan 9, 2024 · Primates exhibit complex brain structures that augment cognitive function. The mammalian brain has distinct structural regions that perform specific functions. 5. "The whole mouse brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a across all mouse strains including NOD/ShiLt, BALB/c, and C57BL/6N. Whole Transcriptome Atlas Profiling : >20,000 genes 5μm FFPE tissue section Area of Illumination (AOI) Profiling Strategy: 360 AOIs total; Geometric profiling in >10 functional areas of the brain Cell type-specific profiling of neurons across cortical layers and other functional areas; Morphology Markers: NeuN – Neurons; GFAP – Astrocytes The Mouse Whole Brain Atlas is a high-resolution transcriptomic and spatial cell-type atlas across the entire mouse brain, integrating several whole-brain single-cell RNA-sequencing (scRNA-seq) datasets. 3483 human genes are missing mouse one-to-one orthologue and is therefore missing mouse expression data in the human protein atlas, expression data based on mouse genes across all mouse strains including NOD/ShiLt, BALB/c, and C57BL/6N. Jun 23, 2017 · Landscape of the mouse transcriptome. S. Isocortex. scc and dyn. et al. Feb 4, 2021 · High-resolution single-cell transcriptome and 3D genome atlas of developing mouse brain • 3D genome “structure types” behind transcriptional cell types • Major transformation of transcriptome and 3D genome after birth, unaffected by experience • Allele-specific 3D structure of imprinted genes, including one that spans a chromosome Dec 1, 2016 · The results show that clustering voxels in the low-dimensional space is more consistent with neuroanatomy than in the original space. Expand. These brain-wide atlases allow for unbiased comparisons between brain regions. S11, A to C). Jul 31, 2023 · Qu et al. To construct a comprehensive spatiotemporal transcriptome atlas at cell type resolution for the human and mouse brain, we initially amassed sc/snRNA-seq data from 19 and 9 peer-reviewed publications originating from the human and mouse brain, respectively (Supplementary Table S1). Our previous adolescent mouse brain atlas did not reveal any splatter-like clusters . Nov 2, 2023 · In this study, we applied a cross-species systems biology approach to large-scale human brain transcriptome data at bulk tissue and single nucleus resolutions, a tau mouse model 18 and Feb 14, 2018 · Lein, E. The whole-brain molecular atlas further supports the identification of the spatial origin of single neurons using their gene expression profile, and forms the foundation to define a minimal gene set - a brain palette - that is sufficient to spatially annotate the adult brain. Oct 1, 2002 · The mouse genome contains about 30,000 genes 2. Each data set is processed through an informatics analysis pipeline to obtain spatially mapped quantified expression information. calcium/calmodulin-stimulated adenylate cyclase 1 [15], a cAMP-synthesizing enzyme. ( 2020) established a molecular atlas to define the spatial organization of adult mouse brain regions. As an illustration of utility, we identify candidate genes that may be related Dec 12, 2023 · In this study, we constructed a comprehensive spatiotemporal developmental atlas of five human brain regions, including Cor, subpallium (Sp), Dien, Mid, and Cere. In 2021, we launched the Allen Institute for Neural Dynamics, a neuroscience division The transcriptome analysis shows that 13731 of the human orthologues (n= 16679) are expressed in the mouse brain, and 763 of these genes show a regionally elevated expression. (A) Transcriptome and epigenome signatures that can be assayed by single cell sequencing, alongside spatial context, connectivity, and physiology. Jul 23, 2020 · The mouse blood-brain barrier transcriptome: a new resource for understanding the development and function of brain endothelial cells. Sep 24, 2019 · Full size image. Dec 14, 2023 · The team's data highlighted more than 5,300 diverse neuronal and non-neuronal cell type clusters falling in almost three dozen classes, 338 subclasses, and 1,201 supertypes, all visualized in an online Allen Brain Cell Atlas resource. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4. 5 mm 2), a mouse hemibrain (∼24. Organism. TLDR. Next, data were log-normalized in dynamo and SCC was performed using dyn. Dec 21, 2023 · However, the regional specification remains largely unexplored during human brain development. 5). We constructed an atlas of >32,000 single-EC transcriptomes from 11 mouse tissues and identified 78 EC subclusters, including Aqp7+ intestinal capillaries and angiogenic ECs in healthy tissues. (a) Percentage of expressed (red, FPKM > = 0. The Allen Mouse Brain Atlas includes a full-color, high-resolution anatomic reference atlas accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures. We discovered that, around GW8, radial glia (RG) cells have Jan 14, 2023 · GEO help: Mouse over screen elements for information. , 2016 ). A metabolome atlas of mouse brain on the global metabolic signature Mar 22, 2024 · The mouse blood–brain barrier transcriptome: a new resource for understanding the development and function of brain endothelial cells. Transcriptional profiling: RNA-Seq Data. We comprehensively characterized spatial-specific changes in gene expression in the aging brain, particularly for isocortex, the Nov 11, 2022 · Comprehensive cellular and molecular taxonomy of cochlea based on scRNA-seq. Wang, Q. We analyzed the expression patterns of over 18,000 transcripts (18,264), mostly corresponding to protein-coding genes, by RNA ISH in the developing wild-type laboratory mouse. 3 million individual brain cells Apr 30, 2020 · A comprehensive atlas of candidate cis -regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2. We identified 27 distinguished brain spatial domains, including layer-specific subregions that are difficult to dissect individually. The transcriptomes of 228,047 individual cells were profiled, and a super-large area spatial atlas (largest to 3 × 4 cm for GW16) of multiple human brain regions was mapped by using Feb 1, 2012 · Su and coworkers reported a gene expression atlas across multiple human and mouse tissues including several mouse brain regions (Su et al. Genome-wide atlas of gene expression in the adult mouse brain. Mar 3, 2018 · The Allen Brain Atlas Cell Types database is an ongoing survey of electrophysiological, morphological, and transcriptomic data derived from individual mouse and human brain cells. From the API, you can: Feb 19, 2024 · Here we generated spatial transcriptomic maps of young and old mouse brains. 5, providing a better understanding of organ development and cellular Oct 1, 2002 · The mouse genome contains about 30,000 genes 2. Anatomical specificity is achieved by Jan 23, 2023 · Fig. In the first stage of this project, we provide genome-wide, exon-level transcriptome data generated using the Mar 26, 2024 · Of the 20175 gene targets contained in the GeoMx Mouse Whole Transcriptome Atlas, 9035 were included in the downstream analyses following QC analysis. However, we observed splatter-like neurons outside the cortex and hippocampus when we included cells that had initially been excluded from that dataset (fig. (2005) A Digital Atlas to Characterize the Mouse Brain Transcriptome. Mar 15, 2023 · Integration of single-cell ATAC-seq mouse brain atlas data 30 with spatial ATAC-seq data facilitated identification of all major cell types, and label transfer was then used to assign cell types Aug 1, 2018 · 2018. purity functions. Dec 12, 2017 · The dataset provides the transcriptome across tissues from three male C57BL6 mice and three male Han Wistar rats. (a) A flow-through hybridization chamber (200 µl volume) composed of a microscope slide loaded with tissue sections, a pair of two 80 µm thick Sep 19, 2012 · A high-resolution anatomical atlas of the transcriptome in the mouse embryo. These features endow the primate brain atlas with a multimodal nature. Explore the design of Mouse WTA in the UCSD genome browser session. PLoS ONE 5 , e13741 (2010). A cellular resolution effort is clearly distinguished Sep 19, 2012 · A transcriptional atlas of the adult human brain is described, comprising extensive histological analysis and comprehensive microarray profiling of ∼900 neuroanatomically precise subdivisions in two individuals, to form a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function. A comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain was generated through examination of chromatin accessibility in 2. We then analyzed the transcriptomes of 50,212 single cells (24,401 young and 25,811 old) derived from the brains of 8 young (2–3 months) and 8 old (21–23 months) mice Dec 1, 2016 · The results show that clustering voxels in the low-dimensional space is more consistent with neuroanatomy than in the original space. . Dec 13, 2023 · Here we report a comprehensive atlas of candidate cis -regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2. (A) Established markers (bold) and markers identified as relevant to the cell type in the literature (italics). 2005). Standardized and computerized annotation of expressio …. Here we performed a single-cell transcriptomic analysis of young and old mouse brains. Brain aging is associated with cognitive decline, memory loss and many neurodegenerative disorders. The allen mouse brain common coordinate framework: a 3D reference Oct 22, 2021 · Spatially resolved transcriptomic technologies are promising tools to study cell fate decisions in a physical microenvironment, which is fundamental for enhancing our knowledge of mammalian development. We obtained four sets of coronal slices (spatial transcriptome sequencing) that approximately corresponded to slices on the Allen Mouse Brain Reference Atlas (ABA) through comparison (Figure 1c). associated with brl results from a loss-of-function mutation in. The neocortex fulfills high-cognitive functions through billions of connected neurons. Nature 445 , 168–176 (2007) ADS CAS PubMed Google Scholar Jan 1, 2021 · Figure 1. a UMAP of 37,384 mice DRG nuclei colored by cell types and annotated by marker genes as indicated in Mar 6, 2023 · The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single- cell RNA-sequencing (scRNA-seq) dataset of ∼7 million cells profiled, and a spatially resolved transcriptomic dataset of ∼4. John Wiley & Sons Inc (2008). Public on Jan 14, 2023. They characterize key cis-elements and TFs during organogenesis and identify a supporting cell type in gonad development. The HBT (Human Brain Transcriptome) project at the Department of Neurobiology Yale University School of Medicine is a public database containing transcriptome data and associated metadata for the developing and adult human brain. By utilizing methylome-based clustering and cross-modality integration with additional BICCN Apr 21, 2017 · Here, we present an atlas of mouse TF DNA-binding activities from 24 adult tissues and 8 fetal tissues ( www. used a computationally efficient implementation of t-SNE, named Barnes-Hut-SNE, to map the sagittal and coronal adult mouse atlas and the brain transcriptome of the six human donors (Fig. PLoS An anatomically comprehensive atlas of the adult human brain transcriptome. May 4, 2022 · So far, we have used Stereo-seq chips of up to an effective area of 13. 1 in at least one sample) and non-expressed (blue, FPKM < 0. They Feb 19, 2024 · Spatial transcriptome (ST) is a recently developed molecular profiling method that measures gene activity with location information in a tissue sample (Stahl et al. , and a genome-wide expression atlas should comprise the spatiotemporal distribution of the entire transcriptome (perhaps including major splice variants) for a series of developmental stages, for adult, and also for relevant disease models. Apr 13, 2022 · To demonstrate the potential for cross-species comparisons, we selected a total of 12 NHP tissues overlapping with single-cell mouse (Mouse Cell Atlas, MCA) and human (Human Cell Landscape, HCL Transcription, Genetic. A transcriptome atlas of the mouse brain at cellular resolution Carson, Thaller and Eichele 563 Figure 1 Equipment developed for automated in situ hybridization and illustration of typical results. (A and B) Distribution and relative expression of individual highly variable genes (violin plots) in endothelium, mesangium, and podocytes. However, the imbalance between resolution, transcript capture and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional Mar 10, 2022 · As GeoMX uses predefined gene panels rather than poly-A capture, Nanostring provides the Cancer Transcriptome Atlas (CTA) gene panel with over 1,800 genes, as well as human and mouse whole Feb 1, 2024 · Explore the Whole Mouse Brain Atlas produced by the BRAIN Initiative Cell Census Network (BICCN) with transcriptomics and other tools. Jun 3, 2023 · To build a single-cell developmental trajectory map of striatal cell types, we integrated previously published striatal single-cell datasets from seven studies that collected data from mouse brain Oct 3, 2018 · All organs were single-cell-sorted into plates using fluorescence-activated cell sorting (FACS), and many were also loaded into microfluidic droplets (see Extended Data and Methods ). 2 cm for different tissue sizes, subdivided into 50, 100, and 200 mm 2 chips for profiling sections from the mouse olfactory bulb (∼10. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled, and a spatially resolved Nov 2, 2015 · Brain transcriptome and connectome maps are being generated, but an equivalent effort on the proteome is currently lacking. Oct 1, 2005 · A Digital Atlas for the Mouse Brain Transcriptome. Single cell (or single nucleus) RNA sequencing (RNA-Seq) is a scalable approach to provide genome-wide expression profiles for thousands of cells. Striatum. 1A, 2A, and S2E ). 3 million individual brain cells from 117 anatomical dissections, unravels the transcriptional regulatory programs that drive the heterogeneity and complexity of brain structure and function. We constructed an atlas of >32,000 single-EC transcriptomes from 11 mouse tissues and identified 78 EC subclusters, including Aqp7 + intestinal capillaries and angiogenic ECs in healthy tissues. tl. Browse the Mouse Whole Transcriptome Atlas Low High Karyogram illustrating the density of genes in the mouse genome. The atlas is hierarchically organized into five nested levels of Jul 7, 2020 · Wan et al. use scRNA-seq and scATAC-seq to profile gene expression and chromatin accessibility in mouse embryos. A key The mammalian brain is complex, with multiple cell types performing a variety of diverse functions, but exactly how each cell type is affected in aging remains largely unknown. Progress in automation of in situ hybridization makes such an atlas possible. , 3. Nature 489 , 391–399 Dec 13, 2023 · The team analyzed the full transcriptome of cells from nearly 100 regions across the mouse brain using high-throughput single-nucleus RNA sequencing, the preferred approach for efforts to create a May 17, 2021 · This sagittal section of a normal adult mouse brain, imaged on the Digital Spatial Profiler, is stained for neuronal protein alpha-synuclein (green) and DNA (blue) to illuminate intricate Sep 23, 2005 · After placing 200 genes into the context of this atlas, the authors illustrate its application in discovering genes potentially involved in diseases and brain development. 0 million cells passing quality control), and a spatial transcriptomic Sep 21, 2023 · The Allen reference atlas: A digital color brain atlas of the C57Bl/6J male mouse. brain samples form the most distinct cluster along PC1. org) In the data set, an average of 290 TFs was identified per tissue, and more Jan 18, 2011 · The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease. Nov 1, 2002 · The construction of the atlas of the human [30][31][32], mouse [33, 34], cattle [3,35], sheep [36], and pig [2] transcriptome provides a comprehensive platform for analyzing the relationship Dec 28, 2022 · Here, we performed a systematic characterization of the changes in molecular signatures and spatial organizations of cells during brain aging by using an experimental approach that combines a single-cell transcriptome imaging method, multiplexed error-robust fluorescent in situ hybridization (MERFISH), 31. Keywords: whole brain, single cell RNA-Seq, transcriptome, mouse: Total Files in Jan 6, 2021 · Using spatially resolved transcriptomics to generate accurate and densely sampled maps of cell types, neuroscientists can expect a resource similar to the original Allen Mouse Brain Atlas, but Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. A single-cell transcriptomic analysis of young and old mouse brains provides a comprehensive dataset of aging-related genes, pathways and ligand-receptor interactions in nearly all brain cell types and reveals that aging, rather than inducing a universal program, drives a distinct transcriptional course in each cell population. Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. ECs from brain/testis, liver/spleen, small intestine/colon, and skeletal muscle/heart pairwise expressed partially overlapping marker genes. In addition, we obtained the expression distribution of some region-related marker genes on ABA slices through a gene search. A genome-wide expression atlas of the nervous system at cellular resolution would be a valuable resource for neurobiology, genetics, developmental biology and medicine. We provide comprehensive datasets of aging-related genes, pathways and ligand This similarity is weak and does not imply a biological category. Dec 13, 2023 · To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq 1, 2 —a recently developed spatial In building the atlas of the P7 mouse brain, we first selected a set of 11 cresyl-violet-stained standard sagittal brain sections that approximate the 11 sagittal sections in Valve-rde’s atlas of the postnatal mouse brain [10]. Jul 29, 2020 · For example, integrating our transcriptome and global epigenomic maps across matched samples showed that the upregulated brain cluster 34 has strong repressive histone mark density (H3K27me3) at May 12, 2022 · Expression profile matrix of adult mouse olfactory bulb were binned into bin 14, mouse brain or mouse embryo were binned into bin 50 (50 × 50 DNB) and the transcripts of the same gene were aggregated within each bin. 1 gene target was removed as a global outlier Feb 20, 2020 · The heterogeneity of endothelial cells (ECs) across tissues remains incompletely inventoried. 2 cm × 13. Using ST, Ortiz et al. By integrated analysis, they provide a cis-regulatory atlas and inferred spatially resolved cis-element profiling of mouse embryos. Jul 6, 2023 · In this study, we used Slide-seq, a technology that generates transcriptome-wide gene expression data at 10-µm spatial resolution 33,39, to build maps of whole embryos during early mouse Mar 22, 2024 · The mouse blood–brain barrier transcriptome: a new resource for understanding the development and function of brain endothelial cells. 3 million individual brain Our focus on neuroscience began with the launch of the Allen Institute for Brain Science in 2003, which led to the creation of the widely-used Allen Brain Atlases. To unveil the gene expression dynamics of cochlear aging at temporal resolution, we constructed a high-throughput scRNA-seq atlas of the mouse cochlea spanning five time points: 1, 2, 5, 12, and 15 months of age ( Figs. The current data include a comprehensive analysis of single cells from one mouse cortical region, primary visual cortex, by scRNA-seq. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. This division is in a 16-year phase focused on multimodal characterization of brain cell types. (B) Comparison of single-cell molecular assays in terms of the number of cells (scope, x axis) and number of unique molecules Dec 13, 2023 · Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. Neuroanatomically precise, genome-wide maps of transcript Jul 15, 2020 · A single-cell transcriptomic atlas across the lifespan of the mouse, denoted Tabula Muris Senis, provides molecular information about the hallmarks of ageing in a range of tissues and cell types. Mahfouz et al. Status. This data set includes single cell and nuclear transcriptomic profiles, assayed from human and mouse brain regions. 2004). yw dz yx fg kh vu fe ve ad lp
