Nature single cell atlas

A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature 587 , 619-625 (2020). ADS CAS PubMed PubMed Central Google Schola Zhang, TQ., Chen, Y., Liu, Y. et al. Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root. Nat Commun 12, 2053 (2021). https.

A molecular single-cell lung atlas of lethal COVID-19 Natur

Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and A single-cell atlas of the peripheral immune response in patients with severe. Collectively, this single-cell protein atlas represents a valuable resource for elucidating metazoan embryogenesis at the molecular and systems levels. You have full access to this article via. Expression profiling on 75,000 single cells creates a comprehensive cell atlas of the human lung that includes 41 out of 45 previously known cell types and 14 new ones Here we compiled an unbiased atlas of human colonic CD8+ T cells in health and ulcerative colitis (UC) using single-cell transcriptomics with T-cell receptor repertoire analysis and mass cytometry

Single-cell transcriptome atlas - Nature Communication

  1. This protocol describes novoSpaRc, a computational pipeline for de novo reconstruction of spatial gene expression from single-cell RNA sequencing with the potential to incorporate spatial atlas.
  2. A single-cell transcriptomic atlas characterizes ageing tissues in the mouse Nature. 2020 Jul;583(7817):590-595. doi: 10.1038/s41586-020-2496-1. Epub 2020 Jul 15. Author Tabula Muris Consortium. Collaborators Tabula Muris Consortium: Nicole Almanzar,.
  3. Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles 1-9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas.Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and.
  4. Here we performed single-cell RNA sequencing of about 10,000 cells from normal liver tissue from nine human donors to construct a human liver cell atlas. Our analysis identified previously unknown subtypes of endothelial cells, Kupffer cells, and hepatocytes, with transcriptome-wide zonation of some of these populations
  5. e the cell-type composition of all major human organs and construct a scheme for the human cell landscape (HCL)
  6. Methods: We have explored the cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. A total of 77,969 cells were collected at 35 distinct locations, from the nose to the 12th division of the airway tree. Measurements and Main Results: The resulting atlas is composed of a high.
  7. A molecular single-cell lung atlas of lethal COVID-19 Nature. 2021 Jul;595(7865):114-119. doi: 10.1038/s41586-021-03569-1. Epub 2021 Apr 29. Authors Johannes C Melms # 1.

A single-cell atlas of the peripheral immune - Natur

A 4D single-cell protein atlas of transcription factors

We perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novel COCH + fibroblasts and FibSmo cells, each of. Harvard University. (2021, June 24). A detailed atlas of the developing brain: Researchers combine single-cell genomic technologies to map the mouse cortex. ScienceDaily. Retrieved August 2, 2021.

A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat Neurosci. 2019 Dec;22(12):2087-2097. PubMed. Recommends. Please to recommend the paper. Comments. Jeremy Miller Allen Institute for Brain Science; Posted: 26 Nov 201 The paper, A molecular single-cell lung atlas of lethal COVID-19, was published April 29 in Nature. The authors (all from Columbia unless noted): Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro (Cornell), Amit Dipak Amin, Denis Schapiro (Harvard and Broad Institute. Figure 1. A Single-Cell Proteomic Atlas of Breast Cancer Ecosystems. (A) Experimental approach. (B) t-SNE plots of EpCAM, CD45, CD31, and FAP expression in 58,000 cells from all samples using a 0 to 1 normalization. (C) t-SNE as in (B), colored by cell type

Single-Cell Atlas of Human Lung Identifies New, Known Cell Types. NEW YORK - Researchers have generated a cellular atlas of the human lung that highlights the more than four dozen cell types residing there using single-cell RNA sequencing. By developing an atlas of lung cells, researchers led by Stanford University School of Medicine's Mark.

Deep in the brain, the striatum receives and coordinates inputs from other parts of the brain. Bocchi et al. surveyed molecular features as the striatum develops in the human brain. Single-cell surveys of long intergenic noncoding RNAs revealed a progenitor for medium spiny neurons and provide insight into evolutionary divergence of this critical part of the brain The first study describes the creation of a single-cell transcriptomic mouse cell atlas that captures cell-type-specific hallmarks across the lifespan of the mouse. The Tabula Muris Senis or Mouse Aging Cell Atlas provides molecular information on age-related changes in specific cell types across 23 tissues and organs A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat. Neurosci. 22 , 2087-2097 (2019) Biology: A single-cell map of the human body. A description of the cell-type composition of all major human organs is presented in Nature. The RNA of over 500,000 single cells from Chinese Han donors was sequenced. These data will contribute to the international effort to complete a human cell atlas. Cells in the human body all carry the same.

A molecular cell atlas of the human lung from single-cell

One can visualize the single-cell gene expression grouped by a specified single-cell metadata. The resulting gene expression can be presented in a (i) bubbleplot where the colour represents the relative gene expression and the bubble size is the proportion of cells in the group expressing the gene, (ii) heatmap where the colour represent the average gene expression in each group, (iii. Single-cell atlas of tumor ecosystem in liver cancer We performed single-cell RNA sequencing (scRNA-seq) of liver tumors to study tumor cell states, cellular hierarchy and its evolution that contribute to ITH ( Figure 1 A and Table S1 ) More information: Jimmy Tsz Hang Lee et al, Fast searches of large collections of single-cell data using scfind, Nature Methods (2021).DOI: 10.1038/s41592-021-01076-

Single-cell atlas of colonic CD8 - Nature Researc

Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root April 2021 Nature Communications 12(1):205 A complete Human Cell Atlas would give us a unique ID card for each cell type, a three-dimensional map of how cell types work together to form tissues, knowledge of how all body systems are connected, and insights into how changes in the map underlie health and disease. New tools such as single-cell genomics have put it within reach. It is. Mulder et al. integrate 178,651 human mononuclear phagocytes (MNPs) from 13 tissues across 41 datasets to generate a MNP single-cell RNA compendium (MNP-VERSE) that enables the definition of conserved gene signatures of MNP populations. This integrated approach provides a robust, online-available platform (https://gustaveroussy.github.io/FG-Lab/) for uniform annotation and dissection of.

Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation. Nature communications , 10 (1), 5462. Human iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of. Advanced NSCLC single-cell atlas. a Graph illustration of the baseline information of the 42 patients, including subtypes, stages, mutation status, and smoking history.b UMAP plot of 90,406 cells from 42 patients, colored by their 11 major cell types.c Heatmap of canonical cell-type markers of 11 major cell types.d UMAP plot of all cells, colored by patients This is the first complete single-cell atlas of human teeth that allows a comparative single-cell RNA analysis of human dental pulp and periodontium. In our data sets, we identified great variability between patients, which was particularly pronounced in the periodontium. The latter could be due to the highly dynamic nature of the periodontiu

NovoSpaRc: flexible spatial reconstruction of single-cell

  1. The Human Cell Atlas initiative has the specific aim of creating a healthy reference map of cells and tissues of the body using single cell genomics and spatial methods. HCA work is not supported by a single funding source but rather via many different funders, some of which are listed in the funding answer above
  2. Credit: Human Protein Atlas. In a study published in the US journal Science Advances, a single cell type map of human tissues is presented. An open access atlas has been launched with more than.
  3. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun. 2019; 10: 4902. 10.1038/s41467-019-12780-8. Google Scholar. Crossref. Search ADS. PubMe
  4. Scientists develop single-cell atlas of the normal human heart. Scientists have for the first time documented all of the different cell types and genes expressed in the healthy human heart, in new.

The Malaria Cell Atlas was established in 2019 as a data resource and website to provide data for researchers to explore gene expression patterns in individual parasites. However, data regarding P. falciparum - the species responsible for most human deaths and disease - has been limited to blood stages. In this study, published in Nature. nature.com - Complex biological processes such as embryogenesis require precise coordination of cell differentiation programs across both space and time. Using A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis - Nature Methods - Flipboar Schistosomiasis is caused by a parasitic flatworm about which little is known. Therefore, options to combat human disease caused by schistosome infection are limited. To aid in our quest to develop treatments, two studies undertook molecular investigations of the parasite Schistosoma mansoni . By generating a single-cell atlas, Wendt et al. identified the developmental trajectory of the. A preview of this full-text is provided by Springer Nature. Learn more; A four-dimensional single-cell atlas of transcription factor expression in Caenorhabditis elegans allows the. They used single-cell RNA sequencing data from tissue samples taken from 11 organ systems—including the lungs, heart, liver, and kidneys—to build a comprehensive cell atlas of hundreds.

A single-cell transcriptomic atlas characterizes ageing

We generated a single-cell tumor immune atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation Brain immune atlas About. The brain immune atlas provides a resource and visualization tool for assessing various single-cell RNA sequencing datasets that together capture the diversity of the brain immune compartment, as published in Nature Neuroscience ([A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment])

7 Single Cell Resources. 7.1 Comprehensive list of single-cell resources; 7.2 Computational packages for single-cell analysis; 7.3 eLife Commentary on the Human Cell Atlas; 7.4 Online courses; References; Published with bookdow The human thymus is the organ responsible for the maturation of many types of T cells, which are immune cells that protect us from infection. However, it is not well known how these cells develop with a full immune complement that contains the necessary variation to protect us from a variety of pathogens. By performing single-cell RNA sequencing on more than 250,000 cells, Park et al. examined.

Human Uterus Cell Atlas. The HUTER project aims to create the single-cell and spatial reference map of the human uterus. HUTER project will provide unprecedented insight at transcriptomic, genomic and spatial changes of this important female organ not only throughout the menstrual cycle but also across lifespan. 2 The team investigated how the SARS-CoV-2 virus interferes with the function of cells and their genetic programs. They used single-cell RNA sequencing data from tissue samples taken from 11 organ systems—including the lungs, heart, liver, and kidneys—to build a comprehensive cell atlas of hundreds of thousands of individual cells showing how COVID-19 can lead to organ failure and death The establishment of the single-cell atlas of the dental pulp and periodontium of human teeth allows further analyses and comparisons at the molecular level between these two tissues (Figures 3 and and4). 4). Therefore, we first proceeded with the comparison between the stem cell clusters detected in these two dental components

the genetic complexity of the disease. Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the first single-cell transcriptomic atlas of the human retina. Using a multi-resolution network Data Availability Statement. Generated scRNA-seq data of MC38 tumor-draining lymph node T cells were deposited in the ArrayExpress database with accession ID E-MTAB-9274.. To construct the reference TIL atlas, we obtained single-cell gene expression matrices from the following GEO entries: GSE124691 25, GSE116390 21, GSE121478 34, GSE86028 67; and entry E-MTAB-7919 71 from Array-Express

A human liver cell atlas reveals heterogeneity and

Although single cell RNA sequencing studies have begun providing compendia of cell expression profiles, it has proven more difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here we describe droplet- and plate-based single cell RNA sequencing applied to ∼75,000 human lung and blood cells, combined with a. , A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment, NATURE NEUROSCIENCE, vol. 22, no. 6, pp. 1021-1035, 2019. @article{8619539, abstract = {{While the roles of parenchymal microglia in brain homeostasis and disease are fairly clear, other brain-resident. Our recent work published in Communications Biology reveals the mammary gland reorganization in lifetime and its link to breast carcinogenesis. The mammary cell atlas resolved at single cell level would provide the research community with a foundation reference to build new data in The human uterus is a highly dynamic tissue that undergoes repeated damage repair and regeneration during the menstrual cycle, which make it ideal model to study tissue regeneration and pathological process. Stem/progenitors were speculated to be involved in the regeneration of endometrial epithelial and pathogenesis of endometriosis. But the identity, microenvironment and regulatory. The Human Cell Atlas is a project to describe all cell types in the human body.The initiative was announced by a consortium after its inaugural meeting in London in October 2016, which established the first phase of the project. Aviv Regev and Sarah Teichmann defined the goals of the project at that meeting, which was convened by the Broad Institute, the Wellcome Trust Sanger Institute and.

Construction of a human cell landscape at single-cell leve

C. elegans is an animal with few cells, but a striking diversity of cell types. Here, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and pre-terminal cell types, mapping most single cell transcriptomes to their exact position in C. elegans' invariant lineage Single-Cell CRISPR Technology Deciphers Role of Chromatin Accessibility in Cancer. Mapping the 'chromatinome': New integrative functional genomics platform for profiling genome regulation with a massively-parallel screen of chromatin modifiers. CRISPR-sciATAC is a novel integrative genetic screening platform that jointly captures CRISPR. The ability of single-cell genomics to resolve cellular heterogeneity is highly appreciated in cancer and is being exploited for precision medicine. In the recent decade, we have witnessed the incorporation of cancer genomics into the clinical decision-making process for molecular-targeted therapies. Compared with conventional genomics, which primarily focuses on the specific and sensitive. Multi-tissue and multi-stage single-cell atlas of COVID-19 patients and healthy controls (A) Flowchart depicting the overall experimental design of this study. Cells circled with dash lines were enriched in samples from the disease progression stage. The comprehensive nature of our dataset proved to be powerful at dissecting the.

Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia April 2021 Nature Neuroscience 24(4):1-1

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. Nature Neuroscience 2019; 22:1021-35. 2 A single cell atlas reveals distinct immune landscapes in transplant and primary tumors that determine response or resistance to immunotherapy Amy J. Wisdom 1 , Yvonne M. Mowery 2,3 *, Cierra S. Hong 1 , Xiaodi Qin 3 , Dadong Zhang 3 , Jonathon E. Himes 1 A molecular single-cell lung atlas of lethal COVID-19 . COVID-19 Autopsy Study Summary. Understanding cellular drivers of lethal SARS-CoV-2 infection is an essential first step towards improving therapies for severe COVID-19. We performed single-nuclei RNA-seq (snRNA-seq) on >116,000 nuclei from 19 COVID-19 autopsy lungs and seven pre-pandemic. Given the importance of the PB for neuroscience studies, its single-cell atlas, particularly the key functional regions such as the cortex and hypothalamus (HT), necessitates elucidation. Leveraging the advantages of pig models, we aimed to gain an in-depth understanding of human neurological disorders and biological processes in the view of.

Shendure Lab

A Single-Cell Atlas of the Human Healthy Airway

  1. A single-cell transcriptomic atlas of the aging mouse brain reveals coordinated and cell-type specific aging signatures across multiple cell populations. Catalogues of gene expression profiles, top marker genes, aging-related genes, pathways and ligand-receptor interactions are reported
  2. EWN Atlas launch event videos. On 15 January, 2019, USACE held a launch event in Washington DC, hosted at the National Building Museum, to mark the publication of the book Engineering With Nature: An Atlas
  3. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. The comprehensive nature of our dataset proved to be powerful at dissecting the associations of age, sex, disease severity, and stage with the diverse immune subsets in SARS-CoV-2 infection. In general, plasma B and proliferative T cells were associated with.
  4. g Interface (API). There are example queries specific to the Cell Types Database available to help you get started
  5. A Single-Cell Tumor Immune Atlas for Precision Oncology. The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision
  6. Single-Cell Expression Atlas Charts Changes in Alzheimer's Entorhinal Cortex. 26 Nov 2019. Most studies of gene-expression changes in Alzheimer's brain analyze tissue samples containing a mix of different cell types. This makes it impossible to definitively figure out the contribution of specific cells. In the November 25 Nature.
  7. To gain a better insight into these processes we have created a single cell transcriptomic atlas across the life span of Mus musculus which includes data from 18 tissues and organs. We discovered cell-specific changes occurring across multiple cell types and organs, as well as age related changes in the cellular composition of different organs

A molecular single-cell lung atlas of lethal COVID-1

  1. Recent advances in single-cell genomic analysis of cells and tissues have put systematic, high-resolution and comprehensive reference maps of all human cells within reach. In other words, we can now realistically envision a human cell atlas to serve as a basis for both understanding human health and diagnosing, monitoring, and treating disease
  2. As embryos develop, numerous cell types with distinct functions and morphologies arise from pluripotent cells. Three research groups have used single-cell RNA sequencing to analyze the transcriptional changes accompanying development of vertebrate embryos (see the Perspective by Harland). Wagner et al. sequenced the transcriptomes of more than 90,000 cells throughout zebrafish development to.
  3. The Yolk Sac (YS) and Aorta-Gonad-Mesonephros (AGM) are two major haematopoietic regions during embryonic development. Interestingly, AGM is the only one generating haematopoietic stem cells (HSCs). To identify the difference between AGM and YS, we compared them using single-cell RNA sequencing between 9.5 and 11.5 days of mouse embryonic development and identified cell populations using.

Single Cell Porta

Publications. Below is the list of papers that are part of the Human Cell Atlas. These have been approved by the HCA Publication Committee (composed of HCA Organising Committee members). The HCA Publication Committee reviews submitted publications to check if they fit within HCA technical scope. This review by the HCA Publication Committee does. Neuroblastoma is a childhood malignancy that originates from neural crest cells. We present a single-cell transcriptome and localization atlas of the developing adrenal gland and identify seven different cell clusters that make up the adrenal medulla. Their transcriptomic profiles were used to generate gene signatures that were compared to neuroblastoma samples

A single-cell atlas of early-stage human brain development is published in Nature Neuroscience this week, providing insights into the first trimester of human brain development and the subpopulations of progenitor cells that form the basis for creating the human cortex. To build the atlas, researchers from the University of California, San. RESEARCH ARTICLE NEURODEVELOPMENT The coding and long noncoding single-cell atlas of the developing human fetal striatum Vittoria Dickinson Bocchi 1,2, Paola Conforti , Elena Vezzoli †, Dario Besusso1,2, Claudio Cappadona 1,2‡,Tiziana Lischetti1,2, Maura Galimberti ,Valeria Ranzani2, Raoul J. P. Bonnal 2§, Marco De Simone ¶, Grazisa Rossetti2§, Xiaoling He3, Kenji Kamimoto4,5,6 A single cell atlas of the malignant and adjacent non-malignant human liver is presented. Recurring stromal cell gene expression signatures are found in liver metastases and cholangiocarcinomas. Tumor and stromal cells communicate through a conserved ligand-receptor interaction network

A Single-Cell Atlas Provides New Details on the Heart. For the first time, researchers have gained unprecedented insight into the function of the healthy human heart by creating an atlas of the various types of cells that compose the heart, and the genes that those cells express. Almost half a million heart cells work in harmony to supply the. Assembly and Exploration of a Single Cell Atlas of the Drosophila Larval Ventral Cord. Identification of Rare Cell Types Rosario Vicidomini, Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland

nature.com - Malaria parasites have a complex life cycle featuring diverse developmental strategies, each uniquely adapted to navigate specific host environments. A single-cell atlas of Plasmodium falciparum transmission through the mosquito - Flipboar To construct an extended single cell atlas of the mammary gland, we profiled cells from late embryogenesis through to post-involution (Fig. 1a). The 10X Genomics Chromium platform was used to create scRNA-seq libraries for mammary epithelial cells across 9 developmental stages, yielding expression profiles for 132,599 cells after quality.

Request PDF | Organoid single-cell genomic atlas uncovers human-specific features of brain development | The human brain has undergone substantial change since humans diverged from chimpanzees and. Kidney glomerular single cell atlas. Here is the web portal for our single cell data reported in paper in press in Nature Communication: Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes. Bing He 1 *, Ping Chen 1 *, Sonia Zambrano 1. MARS is a tool for identifying and annotating cell types across heterogeneous single-cell experiments. MARS has a unique ability to discover and suggest human-interpretable names to novel cell types that have never been seen in previously annotated experiments. The automated assignment of cells to cell types in a new single-cell experiment is.

A single-cell atlas of mouse brain macrophages reveals

Conventional IHC for the integrated single cell atlas of endothelial cells of the human lung. Zenodo. Posted online May 26, 2021. doi: 10.5281/zenodo.4503718 Google Scholar; 9. Habermann AC, Gutierrez AJ, Bui LT, Yahn SL, Winters NI, Calvi CL, Peter L, Chung MI, Taylor CJ, Jetter C, et al. nature.com - Human organogenesis remains relatively unexplored for ethical and practical reasons. Here, we report the establishment of a single-cell transcriptome A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion - Flipboar DOI: 10.1016/j.cell.2019.03.005 Corpus ID: 108293124. A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer @article{Wagner2019ASA, title={A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer}, author={J. Wagner and M. Rapsomaniki and St{\'e}phane Chevrier and T. Anzeneder and C. Langwieder and August Dykgers and M. Rees and A. Ramaswamy and S. A new software tool allows researchers to quickly query datasets generated from single-cell sequencing. Users can identify which cell types any combination of genes are active in. Published in.

Single-cell RNA-seq is worth long-read sequencing | Nature

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. Nature Neuroscience 2019; 22:1021-35. Human and mouse Glioblastoma immune atlas. Ana Rita Pombo Antunes, Isabelle Scheyltjens, Francesca Lodi, Julie Messiaen, Asier Antoranz, Johnny Duerinck, Daliya Kancheva. In a separate study, also appearing today in Nature, researchers from Newcastle University generated a different single-cell liver transcriptome atlas. Theirs focused on how the blood and immune system develop in fetuses Single-cell technologies. Recently, researchers at the Karolinska Institute in Sweden have generated a comprehensive molecular atlas of brain development in mouse embryos. Their study has been published in Nature. The researchers conducted droplet-based single-cell RNA-seq on embryonic mouse brains every day between gastrulation and birth

The single-cell pathology landscape of breast cancer | NatureAlveolar regeneration through a Krt8+ transitional stemOrganoid single-cell genomic atlas uncovers human-specificXiaowei Zhuang: Mapping the transcriptome | Department of

Single Cell Atlas of COVID-19 Affected Cells Created to Help Future Research. May 3, 2021. 315. 3D Rendering, COVID-19 virus infection of human lungs. A large collaboration of U. S. scientists, led by the Broad Institute, has created a single cell atlas to represent the impact severe COVID-19 can have on different cell types around the body We created a single-cell transcriptome atlas of the VNC using single-cell RNA-sequencing with 10x Chromium chemistry. We processed 80 VNCs, 20 per independent replicate (Figure 1A; see Materials and methods).The data were filtered according to the number of genes (nGene), the number of unique molecule identifiers (nUMI), and the proportion of mitochondrial genes (prop.mito) (Figure 1—figure. Single-cell RNA sequencing (scRNA-seq) is the leading technique for charting the molecular properties of individual cells. The latest methods are scalable to thousands of cells, enabling in-depth characterization of sample composition without prior knowledge. However, there are important differences between scRNA-seq techniques, and it remains unclear which are the most suitable protocols for. Recent efforts seek to create a comprehensive cell atlas of the human body [1, 2].The advent of single-cell and single-nucleus mRNA sequencing (RNAseq) in droplet format [3,4,5] now enables large-scale sampling of cells from any tissue, and clustering of these large-scale datasets enables cell type and subtype classification [3, 6,7,8].However, the human body contains orders of magnitude more.