Tag: snRNA-seq

Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution | Molecular Neurodegeneration

Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…

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Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing

Preferential carbohydrate import and early metabolism in PCs (but not SCs) supports renal physiology independent of ATP production Drosophila renal (Malpighian, MpT) tubules consist of two major cell types, the larger PCs and smaller SCs which perform distinct roles in ion, solute and water transport (Fig. 1a, b)16. These functional differences…

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Challenges of profiling motor neuron transcriptomes from human spinal cord

Published in Neuron, Cell Press (Reed Elsevier) Content Single-nucleus RNA sequencing (snRNA-seq) is a powerful approach to study cellular heterogeneity within and across tissues. We and others have previously performed snRNA-seq on adult mouse spinal cord.1,2 To begin to investigate human motor neurons, we performed a pilot snRNA-seq experiment on…

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What key technical adaptation to standard bulk RNAseq methods has enabled transcriptome profiling at the single-cell level?

How can transfer learning be used to cluster single-cell RNA-seq data across species and batch?5 answersTransfer learning can be used to cluster single-cell RNA-seq data across species and batch. SATURN is a deep learning method that learns universal cell embeddings by encoding genes’ biological properties using protein language models. By…

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Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer’s disease dataset

doi: 10.7554/eLife.90214. Affiliations Expand Affiliations 1 UK Dementia Research Institute at Imperial College London, London, United Kingdom. 2 Department of Brain Sciences, Imperial College London, London, United Kingdom. Item in Clipboard Alan E Murphy et al. Elife. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.7554/eLife.90214. Affiliations 1 UK…

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what should I do if I get a compromised sample of scRNA-seq data?

what should I do if I get a compromised sample of scRNA-seq data? 0 Hi everyone, Recently, I got my snRNA-seq data. But after aligned to reference genome using cellranger, I got a wired barcode rank plot. what should I do next to correct this data? Thanks in advance scRNA-seq…

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Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq

Abstract Background: Alzheimer’s disease is the most common cause of dementia and is characterized by amyloid-β plaques, tau neurofibrillary tangles, and neuronal loss. Although neuronal loss is a primary hallmark of Alzheimer’s disease, it is known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis and neuronal health…

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Epigenetic Changes Dictate Cancer’s Course

Understanding the intricate interplay between genetics and cancer progression has long captivated the scientific community. While genetic mutations have been the main focal point in oncology, recent strides have illuminated the profound influence of epigenetic modifications in the development of cancer. In a recent study published in the journal Nature,…

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Immune Response, Metabolism Differences May Explain Increased Risk of Alzheimer’s Among Women

New research published in Alzheimer’s and Dementia found that differences in microglial “immunometabolism endophenotypes”, defined by interactions between immune and metabolic reactions in the brain, may contribute to the pathogenesis and disease progression of Alzheimer’s disease (AD) in females.1 Although women comprise a higher proportion of AD cases than men,…

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snRNA-seq GCC | Frederick National Laboratory

Research Category Research & Development Services & Subcontracts Solicitation Number S24-009 NCI OA Contract Number HHSN261201500003I – IDIQ Description The objectives of this work are for the Offeror generate high quality snRNA-seq data from archived tumor biospecimens for downstream identification and analysis of tumor and immune cell clusters following current…

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snRNA-seq of mouse brain cortex – Project

 Home Project CNP0003558   Source:  CNGB Project  ( ID CNP0003558 ) Project name: – Description: – Data type : – Sample scope: – Relevance: – Submitter: –    Organization: – Related RefSeq Project: – Accession in other database: – Literature(s): – Release date: – Updated: – DOI: – Statistic: Assembly: – Sample: –…

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Deconvolution using cibersortx, help with real example

Hello Biostars, I have been stuck on an issue for quite some time now, and I hope someone can help me or point me in the right direction. I’ve received my bulk RNA fastq files and analyzed it in R using DESeq2. I have found an article that provide snRNA-seq…

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The Imageable Genome | Nature Communications

For the Imageable Genome project, we developed a data pipeline that identifies texts containing radiotracers, recognizes and extracts names of radiotracers from texts, filters for clinically relevant radiotracers and their associated targets, and translates protein names, i.e. of radiotracer targets, to names of the coding genes. We then downloaded the…

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Pioneering study finds predictive biomarker in lung adenocarcinoma

In a recent study published in Nature Communications, researchers from the United States of America (USA) investigated the potential of the transcriptome of tumor-adjacent normal lung tissue in predicting the prognosis of lung cancer. They found that molecular profiling of the tumor-adjacent normal (TAN) lung tissue, rather than the tumor…

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Chst9 Marks a Spatially and Transcriptionally Unique Population of Oprm1 -Expressing Neurons in the Nucleus Accumbens

Abstract Opioids produce addictive, analgesic, and euphoric effects via actions at mu opioid receptors (μORs). The μOR is encoded by the Oprm1 gene and is expressed in multiple brain regions that regulate reward and motivation, such as the nucleus accumbens (NAc). Oprm1 expression in NAc medium spiny neurons (MSNs) mediates…

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Single-cell dynamics of liver development in

image:  Integrated map of scRNA-seq and snRNA-seq data from pig livers at four time points and cellular heterogeneities within each major hepatic cell types. view more  Credit: ©Science China Press This study is led by Prof. Lusheng Huang (National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural…

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Adipose tissue single nucleus RNAseq data

Adipose tissue is usually classified on the basis of its function as white, brown or beige (brite)1. It is an important regulator of systemic metabolism, as shown by the fact that dysfunctional adipose tissue in obesity leads to a variety of secondary metabolic complications2,3. In addition, adipose tissue functions as…

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Postnatal Pig Liver Development Explored Through Single-Cell Dynamics

This study is led by Prof. Lusheng Huang (National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University). Liver executes essential metabolic and immunological functions throughout the postnatal periods, while cellular basis underlying postnatal liver development remains limited. Single cell technology facilitates the study of development at…

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When Glia Meet Induced Pluripotent Stem Cells (iPSCs)

Abstract The importance of glial cells, mainly astrocytes, oligodendrocytes, and microglia, in the central nervous system (CNS) has been increasingly appreciated. Recent advances have demonstrated the diversity of glial cells and their contribution to human CNS development, normal CNS functions, and disease progression. The uniqueness of human glial cells is…

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cGAS-STING triggers inflammaging-associated neurodegeneration | Molecular Neurodegeneration

cGAS-STING triggers inflammaging-associated neurodegeneration In their recent article in Nature, Gulen et al. [1] established the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway as a regulatory driver of inflammaging-associated neurodegeneration in mice. Pharmacological blockade of this pathway in aged mice prevented inflammaging and improved cognitive and motor performance….

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Cellular plasticity of the bone marrow niche promotes hematopoietic stem cell regeneration

Ding, L., Saunders, T. L., Enikolopov, G. & Morrison, S. J. Endothelial and perivascular cells maintain haematopoietic stem cells. Nature 481, 457–462 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Ding, L. & Morrison, S. J. Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches. Nature 495,…

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Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages

Total Sdic mRNA abundance positively correlates with Sdic copy number in testis Evidence for the presumed enhancing effect of gene duplication on the amount of gene product is mixed. Some studies indicated that no such, or a very limited, effect exists19,38,39,40,41, whereas others found a significant increase17,18,22,42,43. A possible explanation…

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Research Reveals Diet, Gene-Linked Obesity’s Impact on Ovarian Health

This study was led by Prof. Zi-Jiang Chen’ team from the Center for Reproductive Medicine of Shandong University, in collaboration with Prof. Fei Gao from the Institute of Zoology, Chinese Academy of Sciences. The researchers employed two types of obese mice induced by environmental and genetic factors as their experimental…

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Tauopathy Transcriptomes Tell Tantalizing Tales

18 Oct 2023 Fibrillar tau accumulates in several neurodegenerative diseases. Are the same molecular mechanisms responsible, or does each tauopathy follow distinct pathways? Some of both, according to a preprint posted to bioRxiv on September 30. Researchers led by Jessica Rexach and Daniel Geschwind at the University of California, Los…

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Behold, the Human Brain Like Never Seen Before

12 Oct 2023 Understanding the human brain has entered a new era with the birth of a comprehensive cell atlas. Scientists used single-cell RNA sequencing, epigenetic analyses, and spatial mapping to study millions of brain cells from 100 brain regions, distinguishing 3,300 cell types. Researchers compared cell types to one…

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Lenvatinib, toripalimab plus FOLFOX chemotherapy in hepatocellular carcinoma patients with extrahepatic metastasis: A biomolecular exploratory, phase II trial (LTSC) | Clinical Cancer Research

Purpose: To investigate the efficacy, safety, and biomarkers of systemic chemotherapy with oxaliplatin, leucovorin and fluorouracil (FOLFOX) in combination with lenvatinib and toripalimab as the first-line treatment for advanced hepatocellular carcinoma (HCC) with extrahepatic metastasis. Patients and Methods: In this biomolecular exploratory, phase II trial, eligible patients underwent the triple…

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Stunning Detail: Single-Cell Studies Chart Genomic Architecture of AD

07 Oct 2023 Why do some people descend into dementia as they age, while others remain sharp? How do genetic variants influence AD pathogenesis? Ditto for the myriad ephemeral states of microglia influence? These are burning questions in AD research these days, and many scientists are looking for answers at…

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Microglial states and their impact on Alzheimer’s disease

In a recent study published in Cell, researchers examined 152,459 microglial transcriptomes from 443 individuals, identifying 12 transcriptional states and their relationship to Alzheimer’s disease (AD). Study: Human microglial state dynamics in Alzheimer’s disease progression. Image Credit: Nefedova Tanya/Shutterstock.com Background Microglia play crucial roles in brain cells, changing states to…

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A subpopulation of lipogenic brown adipocytes drives thermogenic memory

Farber, D. L., Netea, M. G., Radbruch, A., Rajewsky, K. & Zinkernagel, R. M. Immunological memory: lessons from the past and a look to the future. Nat. Rev. Immunol. 16, 124–128 (2016). Article  PubMed  Google Scholar  Netea, M. G. et al. Defining trained immunity and its role in health and…

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Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas | Acta Neuropathologica Communications

Single-nuclei RNA-sequencing analysis of NF1-associated plexiform neurofibroma reveals specific non-neoplastic and neoplastic cellular subpopulations Single-nuclei RNA-sequencing (snRNA-seq) was performed on 8 bulk frozen PN patient samples capturing approximately 4,000 nuclei per sample, a sufficient number of nuclei to provide adequate coverage to report the high levels of cellular heterogeneity found…

Continue Reading Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas | Acta Neuropathologica Communications

Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas

doi: 10.1186/s40478-023-01639-1. Vladimir Amani  1   2 , Kent A Riemondy  3 , Rui Fu  4 , Andrea M Griesinger  5   6 , Enrique Grimaldo  5   6 , Graziella Ribeiro De Sousa  5   6 , Ahmed Gilani  7 , Molly Hemenway  6 , Nicholas K Foreman  5   6 , Andrew M Donson #  5   6…

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Bioconductor – WeberDivechaLCdata

DOI: 10.18129/B9.bioc.WeberDivechaLCdata   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see WeberDivechaLCdata. Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples Bioconductor version: 3.16 Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus…

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Revisiting an Alzheimer’s disease snRNA-Seq dataset

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Compositional analysis in the Human snRNA-seq data

Paired vs Unpaired t-test: Compositional analysis in the Human snRNA-seq data 0 Hi all, I have a 6 case and 6 age-, gender-matched control human brain snRNA-seq data (one-to-one matched). All samples were integrated and analyzed together, and I would like to compare the difference in cell proportion between control…

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Molecular control of endurance training adaptation in male mouse skeletal muscle

A surprisingly low number of genes define the trained muscle To study differences between untrained and endurance-trained muscles (in the present study, muscle always refers to quadriceps), mice were exercised by treadmill running on 5 d per week for 1 h. After 4 weeks, a significant improvement in running performance was observed (Extended…

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Bioconductor – TREG

DOI: 10.18129/B9.bioc.TREG   Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data Bioconductor version: Release (3.17) RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene…

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Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

Consensus MTG taxonomy across primates The BRAIN Initiative Cell Census Network26 generated high-resolution transcriptomic maps of the MTG in human, chimpanzee, gorilla, macaque and marmoset by applying single-nucleus transcriptomic (snRNA-seq) assays to samples isolated from between three and seven donor brains in each species (plate-based SMART-seq v4 (SSv4) for great…

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Potential therapeutic target for chronic kidney disease

TLTs are suggested to directly injure the proximal tubules and promote their proinflammatory property via producing cytokines such as interferon gamma and tumor necrosis factor alpha. Credit: Hiroko Uchida/Kyoto university Chronic kidney disease is a condition in which kidney function declines, causing significant health issues in patients. A previous study…

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Avoiding false discoveries: Revisiting an Alzheimer’s disease snRNA-Seq dataset

Reviewer #1 (Public Review): Murphy, Fancy and Skene performed a reanalysis of snRNA-seq data from Alzheimer Disease (AD) patients and healthy controls published previously by Mathys et al. (2019), arriving at the conclusion that many of the transcriptional differences described in the original publication were false positives. This was achieved…

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Research reveals how the brain sets your body’s dinner clock

SCN snRNA-seq reveals minimal alteration of circadian genes during SF. Credit: Science Advances (2023). DOI: 10.1126/sciadv.adh9570 When you eat is just as important as what you eat. Many people consume their biggest meal of the day at dinner, when it’s after dark and they’re unwinding. But science has shown that…

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Hemocyte Nuclei Isolation from Adult Drosophila melanogaster for snRNA-seq

doi: 10.1007/978-1-0716-3437-0_4. Affiliations Expand Affiliations 1 Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany. 2 Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany. 3 Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany. kpaeschk@uni-bonn.de. 4 Institute of Neuropathology, Faculty of Medicine, University…

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Stem Cell Studies Suggest Mechanism by Which Gene Increases Risk of Sporadic Alzheimer’s Disease

A research team headed by investigators at Brigham and Women’s Hospital reported on the results of a study in which they used stem cells from Alzheimer’s disease (AD) patients to identify a potential mechanism by which a gene known as SORL1 may impact the risk for the neurodegenerative disorder. Their…

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Study shows how brain rhythms can affect brain function by altering microglia and cytokines

Microglial cells, the primary immune cells of the brain and central nervous system, are known to undergo striking morphological changes in response to sensory or neural stimuli. However, the mechanisms and specific signals which cause these changes remain unknown. Study: Brain rhythms control microglial response and cytokine expression via NF-κB…

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Study identifies characteristics specific to human brains

Human-specific gene regulatory changes in the oligodendrocyte lineage. a, The proportions of HS regulatory changes to HS + CS regulatory changes are higher in OPCs than in MOLs (left: snRNA-seq, right: snATAC-seq) for posterior cingulate cortex. P value: chi-square test, two-sided. b, The same as in a, except using the anterior cingulate cortex…

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snRNA seq analysis – huge computational demand due to large number of entries

snRNA seq analysis – huge computational demand due to large number of entries 1 Hello Everyone: I have been conducting single nuclear RNA sequencing (snRNA-seq) analysis of data downloaded from gene expression omnibus (GEO). (The accession number of the dataset is GSE200366, which is a mouse dataset) I have used…

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Understanding plant pathogen interactions using spatial and single-cell technologies

Plants can be infected by diverse pathogenic organisms that modulate host cells to enable their growth and dissemination. Pathogens deploy a variety of manipulation strategies that can vary during the course of infection. These strategies include plant defense suppression as well as deployment of toxins and degradative enzymes to facilitate…

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sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human subcutaneous and visceral adipose tissues

Abstract Deconvolution algorithms rely on single-cell RNA-sequencing (scRNA-seq) data applied onto bulk RNA-sequencing (bulk RNA-seq) to extract information on the cell-types composition and proportions comprising a certain tissue. Adipose tissues cellular composition exhibits enormous plasticity in response to weight changes and high variance at different anatomical locations (depots). However, adipocytes,…

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Unlocking the Secrets of the Macaque Cortex

Recently, close to 100 scientists successfully mapped the cellular taxonomy of the macaque cortex, spotlighting vital relationships between composition and different primate brain regions. To reach this milestone, the team utilized the self-developed spatial transcriptome sequencing technology, known as Stereo-seq, alongside snRNA-seq technology. These cutting-edge tools have provided a…

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Spatial Transcriptomics Creates Comprehensive Atlas of Macaque Cortex

A comprehensive cell-type taxonomy has been constructed for the entire macaque cortex using spatial transcriptomics (BGI’s Stereo-seq technology) and snRNA-seq technology. Through this work, researchers have revealed the relationship between cell-type composition and various primate brain regions. Deciphering the composition and spatial distribution patterns of cell subtypes in the cortex…

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World’s First Single-Cell Spatial Transcriptome of Macaque Cerebral Cortical Cells Released | International

Jul 15, 2023, 03:55PM ISTSource: AP The world’s first single-cell spatial transcriptome of macaque cerebral cortical cells was released. The completion of the mapping is a milestone for cerebral studies. The international academic journal Cell published this important breakthrough led by Chinese scientists online on Wednesday night.The research team divided…

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Scientists map single-cell spatial distributi

A team of nearly 100 scientists recently mapped the cell-type taxonomy in the macaque cortex and revealed the relationship between cell-type composition and various primate brain regions by using the self-developed spatial transcriptome sequencing technology Stereo-seq and snRNA-seq technology, which provides a molecular and cellular basis for further investigation into neural circuits.  The study was…

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Anatomical and molecular characterization of parvalbumin-cholecystokinin co-expressing inhibitory interneurons: implications for neuropsychiatric conditions

Genetic targeting of CCK+ interneurons restricted by the Dlx5/6 driver line in mouse hippocampus and neocortex CCK isoforms and their preprohormone can be expressed in excitatory neurons in addition to GABAergic interneurons [28]. In order to target CCK+ inhibitory interneurons only, we employed an intersectional genetic strategy by simultaneous co-expression…

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Human Heart Cell Atlas Highlights Cardiac Functions, Drug Targets

NEW YORK – An international team of researchers has put together an atlas of the human heart that spells out transcriptomic and chromatin accessibility features in individual, spatially mapped cells across eight distinct areas. “In this study, we charted eight regions of the human heart and provided the most detailed…

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International Scientists Release Most Complete Primate Brain Cell Atlas to Date

The research paper “Single-cell spatial transcriptome reveals cell-type organization in macaque cortex” was published in Cell. Overall experimental design. Spatial distribution map of cell types in the macaque cortex. Database of cell types and gene expression in the macaque cortex BGI’s Stereo-seq Technology Helps Scientists Create the World’s First Three-Dimensional…

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ambient RNA quality control in scRNA-seq

ambient RNA quality control in scRNA-seq 0 Hi all, In scRNA-seq analysis, nCount_RNA and nFeature_RNA value of one sample is very high compared to other samples. (below figure) Also, ‘Fraction Reads in Cells’ in this sample are 70.1%, but do not have a steep cliff in this sample’s web summary…

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Whole genome sequencing across clinical trials identifies rare coding variants in GPR68 associated with chemotherapy-induced peripheral neuropathy

Background: Dose-limiting toxicities significantly impact the benefit/risk profile of many drugs. Whole genome sequencing (WGS) in patients receiving drugs with dose-limiting toxicities can identify therapeutic hypotheses to prevent these toxicities. Chemotherapy-induced peripheral neuropathy (CIPN) is a common dose-limiting neurological toxicity of chemotherapies with no effective approach for prevention. Methods: We…

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Transcriptomics Uncover Vascular Changes in Alzheimer’s Brain

21 Jun 2023 How the brain’s intricate vasculature deteriorates during Alzheimer’s disease has only recently come into focus, thanks to advances in isolating and studying cerebrovascular cells. In a single-nucleus RNA sequencing analysis published in the June 1 Nature Neuroscience, researchers led by Li-Huei Tsai and Manolis Kellis at Massachusetts…

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MULTI-seq Sample Multiplexing for Single Cell Analysis and Sequencing

Single-cell RNA-seq (scRNA-Seq) is a powerful but relatively low-throughput tool to analyze gene expression at the single-cell level. Discover our new MULTI-seq system, developed to multiplex sample types using lipid-modified oligonucleotides (LMOs) complexed with unique DNA sample barcodes, allowing for multiple samples to be pooled together in the same single-cell…

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Aging Fly Cell Atlas Reveals Patterns of Gene Expression in Different Cell Types

As the body ages, organ function progressively declines and the risk for a wide range of diseases, including cardiovascular disease, cancer, and neurodegenerative diseases increases. Understanding how the body ages is an intense area of research as it could potentially indicate ways to promote healthy aging. An international research effort…

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Avoiding false discoveries: Revisiting an Alzheimer’s disease snRNA-Seq dataset

Abstract Arising From: Mathys, H. et al. Nature (2019). doi.org/10.1038/s41586–019–1195–2 Mathys et al., conducted the first single-nucleus RNA-Seq study (snRNA–Seq) of Alzheimer′s disease (AD). The authors profiled the transcriptomes of approximately 80,000 cells from the prefrontal cortex, collected from 48 individuals – 24 of which presented with varying degrees of…

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Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program

Common variants associated with TAAD We designed a two-phased GWAS. The initial MVP discovery analysis was composed of 8,626 individuals (7,050 European, 1,266 African and 310 Hispanic ancestry participants) with TAAD and 453,043 disease-free individuals from the same ancestral groups (Supplementary Fig. 1); their baseline characteristics are presented in Supplementary…

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SENIOR RESEARCH SPECIALIST job with University of Missouri – Columbia

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…

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Open PhD position in Bioinformatics

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…

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Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data

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…

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Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing | BMC Cancer

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…

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High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq

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…

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Novel Multiple Sclerosis Biological Pathway Uncovered

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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IJMS | Free Full-Text | SnRNA-Seq of Pancreas Revealed the Dysfunction of Endocrine and Exocrine Cells in Transgenic Pigs with Prediabetes

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of…

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Multiomics eye study identifies genes with age-related macular degeneration risks

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…

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Age-Related Macular Degeneration Risk Genes, Pathways Found in Multiomics Eye Study

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…

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The Biostar Herald for Monday, April 17, 2023

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…

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How do we know if our brain is capable of repairing itself?

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…

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Researchers construct a high-resolution single-nucleus RNA sequencing (snRNA-seq) analysis of gene expression changes across all brain cell

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,…

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Cell mapping and ‘mini placentas’ give new insights into human pregnancy

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…

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Meet DiNiro: An Interactive Platform for Single-cell RNAseq-based Gene Regulatory Network Analysis

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…

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Single-nuclei RNA sequencing (snRNA-seq) uncovers trophoblast cell types and lineages in the mature bovine placenta

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…

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Purkinje-Enriched snRNA-seq in SCA7 Cerebellum Reveals Zebrin Identity Loss as a Central Feature of Polyglutamine Ataxias

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…

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NAD+ precursor supplementation prevents mtRNA/RIG-I-dependent inflammation during kidney injury

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…

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The gut microbiome modulates the transformation of microglial subtypes

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)….

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Exploring the gene regulatory dynamics of the maturing human brain

  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…

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Alzheimer’s Gene MS4A4A Governs the State of Microglia

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…

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Apolipoprotein E4 promotes the development of Alzheimer’s disease

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…

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Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases

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…

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Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits

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…

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Genome editing prevents hypertrophic cardiomyopathy in mice

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…

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Single-Nuclei Multi-omics Spots Wonky Gene Regulation

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…

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Liver cells that intensify the progression of nonalcoholic fatty liver disease isolated

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…

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Nonalcoholic Steatohepatitis Linked to Inflammation-Related Liver Cell Signature

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…

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Multiplexed snRNA-seq from frozen human brain samples

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…

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Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue

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…

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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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