Tag: snRNA-seq

Hiring Department Dalton Cardiovascular Research Center Job Description Provides technique support of the cardiovascular research program. Requires advanced expertise in molecular and cellular biology, and bioinformatics analysis in the cardiovascular system. Techniques required include, but not limited to primary cultures of cardiovascular cells, genetical manipulation in vitro such as gene…

München   The Beltrán and Kerschensteiner Labs at the Biomedical Center of the Ludwig-Maximilians University Munich are looking for a PhD student in Bioinformatics. The candidate will develop bioinformatic methods for integrative analysis of scRNA-seq and snRNA-seq datasets from multiple sclerosis (MS) human samples and related MS models. Such integrative…

doi: 10.1093/biostatistics/kxad010. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA. 2 Department of Genetic Medicine, Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA. Item in Clipboard Albert Kuo et…

Single-cell and single-nucleus RNA sequencing of sarcoma subtypes In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing sarcoma (ES), and desmoplastic small round cell tumor (DSRCT) (Fig. 1). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ…

Overview of the droplet-based snRandom-seq method for FFPE tissues The main workflow of snRandom-seq is shown in Fig. 1. For single nucleus isolation of FFPE tissues, the areas of interest of banked FFPE tissue block were first selected and placed into tubes. Deparaffinization and rehydration were carried out with standard xylene…

Researchers at Mount Sinai have discovered that cross-talk between brain cells and peripheral immune cells can modulate the progression of multiple sclerosis (MS). The findings reveal a previously unknown way in which the brain and immune system talk to each other and may identify a new therapeutic target for MS…

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A team of researchers used gene expression, epigenetic, and gene regulation analyses to discover genes, pathways, and regulatory features relevant to age-related macular degeneration (AMD). (Image Credit: Adobe Stock/catalin) A team led by investigators at the University of Utah, Genentech, and the State University of New York at Buffalo used…

NEW YORK – A team led by investigators at the University of Utah, Genentech, and the State University of New York at Buffalo has used gene expression, epigenetic, and gene regulation analyses of human eye tissues to discover genes, pathways, and regulatory features relevant to age-related macular degeneration (AMD). “Our…

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

Estimating the appropriate power for sc/snRNA-seq studies of human AHN(A) Summary of the published snRNA-seq studies in adult human hippocampus.(B) Probability estimation using How Many Cells|Satija Lab online software (satijalab.org/howmanycells/) assessing how many cells need to be sampled to detect at least n cells of each type. For a given…

in Data Sets, Publications 4 days ago 413 Views This paper by co-first authors JinChao Hou, PhD, and Yingyue Zhou, PhD, postdoctoral researchers in the Colonna Lab WUSTL, presents a high-resolution single-nucleus RNA sequencing (snRNA-seq) analysis of gene expression changes across all brain cells during demyelination and remyelination induced by cuprizone,…

Trophoblast cell states in the early maternal–fetal interface. a, Schematic representation of the maternal–fetal interface during the first trimester of human pregnancy. b, Histological overview (haematoxylin and eosin (H&E) staining) of the implantation site of donor P13 (approximately 8–9 PCW) (n = 1). Black outlines indicate trophoblast microenvironments in space. c, Uniform manifold…

Scientists from the University of Hamburg, Germany, have developed a novel methodology, DiNiro, for unraveling differential regulatory disease mechanisms from single-cell RNA-seq data. Computational tools for analyzing differential gene expression profiles and differential pathway expression have been previously developed. DiNiro is the first known method based on single-cell data for…

Ruminants have a semi-invasive placenta, which possess highly vascularized placentomes formed by maternal endometrial caruncles and fetal placental cotyledons and required for fetal development to term. The synepitheliochorial placenta of cattle contains at least two trophoblast cell populations, including uninucleate (UNC) and binucleate (BNC) cells that are most abundant in…

Abstract Spinocerebellar ataxia type 7 (SCA7) is a dominantly inherited neurodegenerative disorder caused by a CAG-polyglutamine repeat expansion in the ataxin-7 gene. SCA7 patients display retinal degeneration and cerebellar degeneration with a striking loss of Purkinje cell neurons as the disease progresses. The normal function of the ataxin-7 protein is…

Altered NAD+ metabolism is prominent in diseased human kidneys We collected human kidney samples from healthy controls (n = 25) and patients with diabetic or hypertensive KD, defined as estimated glomerular filtration rate (eGFR) less than 60 ml min−1 per 1.73 m2 and kidney fibrosis (n = 25) (Fig. 1a). The mean eGFR values were 95 ml min−1 per 1.73 m2 (healthy…

Single-cell nucleus RNA-seq profiling of Hip and PFC A schematic of nuclei isolation and the snRNA-seq workflow from the Hip and PFC is shown in Fig. 1a. Using the droplet-based single-nucleus method, we captured 72,226, and 67,698 nuclei from the Hip and PFC, respectively, in the 9 mice (3 per group)….

  Abstract: The human brain develops gradually overtime where distinct molecular profiles are established in the embryo. These molecular profiles continue to change through aging and in response to environmental factors. The complexity and dynamics of gene expression and regulation at the cell type-specific level are still poorly understood, especially…

03 Mar 2023 Of the dozens of loci genome-wide association studies have linked to Alzheimer’s, most are mysterious to scientists. How do they contribute to disease? Much work focuses on changes in expression of individual genes, but as reported in a preprint posted to medRxiv on February 8, scientists led…

In a recent study published in Nature Aging, researchers characterize the effects of neuronal apolipoprotein E4 (APOE4) on Alzheimer’s disease (AD)-associated pathology in tauopathy mice expressing APOE4. Study: Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits. Image Credit: Marko Aliaksandr / Shutterstock.com What is APOE4? APOE4 is a strong…

Harmonizing datasets for eQTL and co-regulation analysis We combined 14 eQTL datasets into the ‘MetaBrain’ resource to maximize statistical power to detect eQTLs and create a brain-specific gene co-regulation network (Fig. 2, Supplementary Figs. 1–7 and Supplementary Table 1). Previous to quality control (QC), MetaBrain includes 7,604 RNA-seq samples and…

Neuron-specific removal of the APOE gene in tauopathy mice Our laboratory previously generated mouse lines expressing a floxed human APOE3 or APOE4 gene45 and a Cre recombinase gene under the control of a neuron-specific synapsin-1 promoter (Syn1-Cre)46. These floxed APOE-KI (fE) mice express homozygous human APOE3 or APOE4 in place…

In a recent study published in the journal Nature Medicine, researchers pursued one-time cures for hypertrophic cardiomyopathy (HCM). They used a previously constructed murine model of HCM, designated as R403Q-129SvEv, to evaluate two different genetic therapies, as follows: i) an adenine base editor (ABE8e) ii) a potent Cas9 nuclease delivered…

10 Feb 2023 Many GWAS variants that raise Alzheimer’s disease risk lie in noncoding stretches of DNA. Do they influence transcription? The answer to this question has been hard to come by, but a new approach might help. Scientists led by Nicholas Cochran, Richard Myers, and Lindsay Rizzardi at HudsonAlpha…

Cell clustering and cluster composition of snRNA-seq on human livers. (A-B) Quality control metrics of snRNA-seq across different samples by violin plot and UMAP plot. (C) UMAP plot visualization of clusters based on group conditions. (D) Violin plot of expression level for signature genes of each cluster. (E) Relative proportion…

NEW YORK – Using single-nucleus transcriptome sequencing and epigenomic profiling, a University of Pennsylvania-led team has teased out liver cell features linked to an advanced form of nonalcoholic fatty liver disease (NAFLD) called nonalcoholic steatohepatitis (NASH), identifying a group of hepatocyte liver cells marked by a cell adhesion- and migration-related…

This is a protocol to save your experiment and successfully demultiplex nuclei using CellPlex, the cholesterol-modified-oligo (CMO) barcodes from 10x Genomics on your nuclei from snap-frozen tissue. Generally speaking, nuclei from snap-frozen tissue perform really poorly with CMOs. This crucial information was not in their initial documentation when the product…

Study overview We established a workflow to compare performance between the 10 × Genomics Chromium NextGEM Single-Cell 3’ and 5’ gene expression kits and evaluate detection of known germline and somatic variants in the resulting datasets (Fig. 1). For these analyses, we obtained frozen resected brain tissue from three pediatric patients treated for…

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…

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…

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…

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…

. 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….

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…

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….

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…

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…

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)….

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…

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…

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…

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…

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…

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…