Tag: snRNA-seq

Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease

The heterogeneity of GABAergic neurons in human, macaque, mouse, and pig To perform a cross-species comparative study of the GABAergic neurons, we collected the snRNA-seq datasets of the cerebral cortex for human10,11, macaque12,13, mouse14,15, and pig16. After cell-type annotation and filtering out the excitatory neurons and non-neurons, the GABAergic neurons…

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Transcriptomic dysregulation across cerebral cortex in autism spectrum disorder

A recent study in Nature demonstrated transcriptomic dysregulation in the cerebral cortex in autism spectrum disorder (ASD). Study: Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD. Image Credit: Ukrolenochka/Shutterstock Background The risk factors for ASD include a significant genetic component with hundreds of risk genes involved. Molecular profiling…

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Challenges of single-cell and single-nucleus RNA-sequencing from core needle biopsy specimens

Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. KU Leuven researchers provide an overview of the technical challenges that should be…

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The Unbreakable Attraction of Mosquitoes to Humans

A female Aedes aegypti  mosquito feeds from a researcher at The Rockefeller University. Credit: © Alex Wild More than a decade ago, Leslie Vosshall, then a relatively new Howard Hughes Medical Institute (HHMI) Investigator, decided to switch from studying innocuous fruit flies to a far deadlier creature—the mosquito. Perhaps her extensive knowledge of…

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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

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Nature Papers on Long Reads for Bacterial Genomes, Zebrafish Atlas, Hypothalamic Aging in Mammals

A study demonstrating the use of long-read Oxford Nanopore sequencing to generate near-finished bacterial genomes from isolates or metagenomes, without short-read or reference polishing, is presented in Nature Methods this week. Oxford Nanopore sequencing has enabled the recovery of highly contiguous microbial genomes from isolates or metagenome but obtaining near-finished…

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Research opens the door to improved treatments for congenital heart disease

Researchers at Baylor College of Medicine, Texas Heart Institute, Texas Children’s Hospital and collaborating institutions have improved our understanding of the mechanisms underlying the progression of congenital heart disease (CHD) – a spectrum of heart defects that develop before birth and remain one of the leading causes of childhood death….

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Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

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Nature Papers on Flying Spider-Monkey Tree Fern Genome, Single-Nucleus Sequencing of Purkinje Cells

The genome of the flying spider-monkey tree fern, Alsophila spinulosa, is reported in Nature Plants this week, providing new insights into tree fern biology. Despite ferns’ high ornamental value and potential as a source of natural products with pharmaceutical applications, little is known about their evolution, with only two small…

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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Modeling injury and repair in kidney organoids reveals that homologous recombination governs tubular intrinsic repair

Submission history Received: 28 May 2021 Accepted: 14 January 2022 Acknowledgments We thank J. V. Bonventre, J. A. Lewis, and E. P. Rhee for institutional support; S. J. Hill for insightful discussion and sharing antibodies; Y. Yoda for cell culture; L. Racusen of Johns Hopkins University for the HKC-8 cell…

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Single-nucleus transcriptional profiling of chronic kidney disease after cisplatin nephrotoxicity

This article was originally published here Am J Pathol. 2022 Jan 26:S0002-9440(22)00013-X. doi: 10.1016/j.ajpath.2021.12.012. Online ahead of print. ABSTRACT Cisplatin induces both acute and chronic nephrotoxicity during chemotherapy in cancer patients. Here, we report the first study of single-nucleus sequencing (snRNA-seq) of cisplatin-induced nephrotoxicity. Repeated low-dose cisplatin treatment (RLDC) led…

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Identification of a regulatory pathway inhibiting adipogenesis via RSPO2

Integration of APC scRNA-seq data reveals heterogeneity of adipocyte progenitor cells In a previous study9, we defined Lin−Sca1+CD142+ APCs as adipogenesis regulatory (Areg) cells and demonstrated that these cells are both refractory toward adipogenesis and control adipocyte formation of APCs through paracrine signaling. In contrast, Merrick et. al.4 observed that Lin−CD142+ cells…

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Cellular and Molecular Atlas of the Macaque Dorsal Horn

Arokiaraj, Cynthia Mary (2022) Cellular and Molecular Atlas of the Macaque Dorsal Horn. Doctoral Dissertation, University of Pittsburgh. (Unpublished) Abstract The spinal cord dorsal horn occupies a key position in the central nervous system, as it is the first site of integration of somatosensory input from the periphery. Local interneurons…

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About ‘Estimated Number of cells’ in snRNA-seq

About ‘Estimated Number of cells’ in snRNA-seq 0 Hi all, I am analyzing single nucleus RNA-seq data using Seurat. And I have total four group and 24 samples (Brain region A Control & case and Brain region B Control & case; each n=6). I wonder what is the appropriate range…

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VisCello Shiny app code for hosting snRNA-seq data

I am trying to set up VisCello shiny app for hosting some of our single cell data, analyzed in Seurat: github.com/qinzhu/VisCello I am using the following code though running into a problem, the app launches however I dont see the umaps and when I click over to differential expression the…

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