Tag: CITE-seq

Confusion about “Top Features table” in cellranger web summary output for CITE-Seq libraries

Confusion about “Top Features table” in cellranger web summary output for CITE-Seq libraries 0 I am reviewing the Web Summary (count) documentation on the 10X genomics website and became confused as to what is being displayed in the Top Features by Cluster table under the Antibody tab (see screenshot below)….

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Bioinformatics Analyst I-II in Seattle, WA for Fred Hutchinson Cancer Center

Details Posted: 17-Dec-23 Location: Seattle, Washington Type: Full-time Salary: Open Overview Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington. With a…

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Bioinformatics Software Engineer Consultant Job at ProCogia

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

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Will Wang speaks in Spatial Multiomics Webinar Series: Enriching Spatial Proteomic Data with Parallel CITE-seq Analysis Elucidates Multiomic Changes with Aging | Blau Lab

Integrating complementary data sets provides a powerful tool to study complex biological processes. In this webinar, Dr. Will Wang from Stanford University will discuss the use of CODEX (Co-Detection by Indexing) spatial proteomic data in parallel with CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) data to study tissue…

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ProCogia hiring Bioinformatics Software Engineer Consultant in Vancouver, British Columbia, Canada

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

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New Method Removes Background Noise from CITE-Seq Data

CITE-seq, short for cellular indexing of transcriptomes and epitopes, employs RNA sequencing to simultaneously measure cell surface protein and transcriptomic data in a single cell readout. Image Credit: Design_Cells/Shutterstock.com The concurrent study of cells provides unprecedented insights into novel cell types, disease states, or other conditions. While CITE-seq addresses the…

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New Method DecontPro Helps Analyze Single-Cell Data With Reduced Background Noise

– Advertisement – New Method Helps With Analysis of Single-Cell Data CITE-seq is a method that quantifies cell surface protein and transcriptomic data within a single cell readout Researchers from Boston University have developed DecontPro, a tool to remove unwanted background noise from CITE-seq data DecontPro can estimate and remove…

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BU researchers develop new method to help wit

(Boston)—CITE-seq (cellular indexing of transcriptomes and epitopes) is an RNA sequencing-based method that simultaneously quantifies cell surface protein and transcriptomic data within a single cell readout. The ability to study cells concurrently offers unprecedented insights into new cell types, disease states or other conditions.   While CITE-seq solves the problem…

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Options for assigning cell labels to barcodes from CITE-seq experiment

Options for assigning cell labels to barcodes from CITE-seq experiment 0 I have barcodes from a CITE-seq experiment that I would like to assign cell labels to. To accomplish this task, I used the Monaco reference database as input into SingleR based on the RNA expression data. I would now…

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Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics

Job:Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics 0 @jp-carter-15371 Last seen 3 hours ago Nashville, TN Creative Data Solutions (Vanderbilt University, Nashville, TN, USA) is seeking a Bioinformatics Research Associate, who will be involved in a variety of life sciences projects and be directly involved in workflows and pipelines…

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Vae_q.latent_space_classifer_ not found in totalVI CITE-seq reference mapping tutorial – scvi-tools

We are following the tutorial located here to create a reference and map cell idents to a query. CITE-seq reference mapping with totalVI — scvi-tools In “Query cell type prediction”, we receive an error that vae_q does not have latent_space_classifier_, when running: predictions = vae_q.latent_space_classifer_.predict(query.obsm[“X_totalvi_scarches”]) Should this be vae instead…

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Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer | Military Medical Research

Zhu J, Ke Y, Liu Q, Yang J, Liu F, Xu R, et al. Engineered Lactococcus lactis secreting Flt3L and OX40 ligand for in situ vaccination-based cancer immunotherapy. Nat Commun. 2022;13(1):7466. Article  CAS  PubMed  PubMed Central  Google Scholar  Evans ER, Bugga P, Asthana V, Drezek R. Metallic nanoparticles for cancer…

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Proteintech Genomics Launches First Commercially Available Solution for the Detection of Intracellular Proteins for Single-Cell RNAseq Experiments

SAN DIEGO–(BUSINESS WIRE)– Proteintech Genomics, a subsidiary of Proteintech Group, Inc., and a provider of multiomic solutions for single-cell and spatial analysis, announced the launch of the MultiPro™ Human Fixed Cell Immune Profiling Antibody Cocktail. This cocktail contains 53 antibodies against intracellular and cell surface proteins, plus 5 isotype controls….

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CRISPR screening in hematology research: from bulk to single-cell level | Journal of Hematology & Oncology

Transcriptomics CROP-seq [46] Jurkat Poly-A CRISPRko Cas9 119 – 5798 (+ 1320 cells with NT gRNA) Lentiviral DROP-seq RNA Perturb-seq [43, 44] K562 Barcode CRISPRi dCas9-KRAB UPR epistasis screen: 9 triplet combinations UPR Perturb-seq experiment: 91 Up to 3 gRNAs in a single vector UPR epistasis screen: 15006 UPR Perturb-seq experiment:…

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CITE-seq data visualization

Hello, I have produced quite some single cell CITE-seq data at the single cell level, using the 10x genomics platform and analyzed in Seurat. I am at the moment trying to visualize the protein markers from the CITEseq against to each other in a way that would resemble how we…

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Luecken Cite-seq human bone marrow 2021 s4d8

Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and Antibody-Derived Tags (ADTs) using the 10X 3′ Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0. All files stored…

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The status of the human gene catalogue

Understanding our Genetic Inheritance: The US Human Genome Project, The First Five Years 1991-1995 (US Department of Health and Human Services, US Department of Energy, 1990). Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022). Describes the first complete gap-free assembly and annotation of…

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CITE-seq reveals inhibition of NF-kB pathway in B cells from vitamin D-treated multiple sclerosis patients

Abstract Vitamin D deficiency is a recognized risk factor for multiple sclerosis (MS) and has been associated with disease activity and progression. Vitamin D treatment has emerged as potentially protective, despite conflicting results from randomized controlled trials. Here, we used single-cell RNA-sequencing (scRNA-seq) combined with barcoded antibodies targeting surface markers…

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Unmapped Reads in Kallisto

Unmapped Reads in Kallisto 1 Hi, I’m using kallisto and bustools for single cell RNA-seq, in a similar way to what is done in the Pall Melsted et. al. paper here: www.biorxiv.org/content/10.1101/673285v1 I’m trying to get an idea of what information is in the reads that aren’t aligned to anything,…

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Allen Institute for Immunology hiring Manager, Bioinformatics Operations – Immunology in Seattle, WA

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact…

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Pythia Biosciences hiring Bioinformatics Data Scientist in United States

“Every scientist is important because every patient is important”. At Pythia Biosciences, we help scientists help patients by offering cutting-edge software and a wide array of complementary services to empower multi-omics data analysis at biotech companies and pharmaceutical organizations.  We are looking for a bioinformatics professional to join us as…

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Bioconductor – CiteFuse

DOI: 10.18129/B9.bioc.CiteFuse   CiteFuse: multi-modal analysis of CITE-seq data Bioconductor version: Release (3.17) CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis,…

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Identification, sorting and profiling of functional killer cells via the capture of fluorescent target-cell lysate

Kagi, D., Ledermann, B., Burki, K., Zinkernagel, R. M. & Hengartner, H. Molecular mechanisms of lymphocyte-mediated cytotoxicity and their role in immunological protection and pathogenesis in vivo. Annu. Rev. Immunol. 14, 207–232 (1996). Article  CAS  PubMed  Google Scholar  Prager, I. & Watzl, C. Mechanisms of natural killer cell-mediated cellular cytotoxicity….

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Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF),…

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Director, Bioinformatics – Immunology Center of Georgia job with Augusta University

Director, Bioinformatics – Immunology Center of Georgia Job ID: 253563Location: Augusta UniversityFull/Part Time: Full TimeRegular/Temporary: * About UsAugusta University is Georgia’s innovation center for education and health care, training the next generation of innovators, leaders, and healthcare providers in classrooms and clinics on four campuses in Augusta and locations across…

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An Inflammatory State Remodels the Immune Microenvironment and Improves Risk Stratification in Acute Myeloid Leukemia

About the webinar   Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive census of the bone marrow immune microenvironment in adult and pediatric AML patients. We characterize unique inflammation signatures in a subset of AML patients associated with…

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A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring

The accurate estimation of cell surface receptor abundance for single cell transcriptomics data is important for the tasks of cell type and phenotype categorization and cell-cell interaction quantification. We previously developed an unsupervised receptor abundance estimation technique named SPECK (Surface Protein abundance Estimation using CKmeans-based clustered thresholding) to address the…

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Multiple organ functions of the yolk sac revealed by early human development map

Multiorgan functions of the human YS. We characterized functions of the developing human YS, combining scRNA-seq and CITE-seq with 2D and 3D imaging techniques. Our findings revealed YS contributions to metabolic and nutritional support and to early hematopoiesis. We characterized myeloid bias in early hematopoiesis, distinct myeloid differentiation trajectories, evolutionary…

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Spatial transcriptomics: recent developments and insights in respiratory research | Military Medical Research

Zepp JA, Morrisey EE. Cellular crosstalk in the development and regeneration of the respiratory system. Nat Rev Mol Cell Biol. 2019;20(9):551–66. Article  CAS  PubMed  PubMed Central  Google Scholar  Kiley JP. Advancing respiratory research. Chest. 2011;140(2):497–501. Article  PubMed  PubMed Central  Google Scholar  Goldstraw P, Ball D, Jett JR, Le Chevalier T,…

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Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Cell culture All cell lines used and derived by different approaches in this study are listed in Supplementary Table 1. Detailed information about the experimental design, materials and reagents is presented in the Reporting Summary. Primary human adult dermal fibroblasts (HDFa) from three different female donors were obtained from Gibco…

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Platelet factors attenuate inflammation and rescue cognition in ageing

Animal models The C57BL/6 mouse line was used for all of the experiments (The Jackson Laboratory and National Institutes of Aging). Homozygous Pf4-KO mice were previously generated and characterized as described48. Pf4-KO mice were a gift from M. Anna Kowalska. Heterozygous mice were bred to generate Pf4-KO and WT littermate…

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In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis

Mouse models C57BL/6J (strain 000664, The Jackson Laboratory) and B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*/-EGFP)Fezh/J (strain no. 026179, The Jackson Laboratory) were used for all experimental procedures. The Npm1c/Flt3-ITD/Cas9 model has been extensively described previously31,57,58. The maximal tumor size allowed by the Home Office license for this project and authorized by the Animal Welfare Ethical…

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Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma

Workflow overview CITE-seq and cell hashing were performed on liquid and solid tissue biopsies (Fig. 1a, b). Experimentally, cells from 17 samples (Supplementary Data 2) were hashed and stained with a panel of 97 antibodies (Supplementary Data 2) covering key as well as exploratory immuno-oncology markers resulting in 57,261 cells after preprocessing and…

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Dissecting human population variation in single-cell responses to SARS-CoV-2

Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…

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Multiparametric senescent cell phenotyping reveals targets of senolytic therapy in the aged murine skeleton

Development and validation of a senescence CyTOF antibody panel We constructed and validated a comprehensive CyTOF antibody panel to include markers for both cell identity and senescent phenotype (Table 1). A defining characteristic of senescent cells is expression of cell cycle inhibitors, in particular p16 or p2129, so we carefully validated…

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A universal tool for predicting differentially active features in single-cell and spatial genomics data

singleCellHaystack methodology For a detailed description of the original singleCellHaystack implementation (version 0.3.2) we refer to Vandenbon and Diez19. In brief, singleCellHaystack uses the distribution of cells inside an input space to predict DAFs. First, it infers a reference distribution \(Q\) of all cells in the space by estimating the…

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counts of cite-seq-count vs. cellrenager varies tremendously

I was wondering if I can still use (trust?) the cite-seq-count tools. The tool was not updated for a few years and I’m not sure, if it is still on the level of for example cellranger. I have tested the 5k_pbmc_protein_v3_nextgem data set from 10x Genomics with CITE-Seq data for…

Continue Reading counts of cite-seq-count vs. cellrenager varies tremendously

To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker measurements with oligo-tagged antibodies.

Dataset Description To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker measurements with oligo-tagged antibodies. To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker…

Continue Reading To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker measurements with oligo-tagged antibodies.

New York Genome Center hiring Postdoctoral Research Associate (Bioinformatics), MacMillan CSNCG in New York, New York, United States

The incumbent Postdoctoral Research Associate will support the “Copy number alterations and epigenetic rewiring in single cells that affect the activity and efficacy of genome-targeting drugs” project as part of the MacMillan Center for the Study of the Non-Coding Cancer Genome (CSNCG). The MacMillan CSNCG is a partnership between The…

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scRNA-seq CITE-seq-count bioinformatics

CITE-seq is a nice method of multiplexing single cell libraries using antibodies. Details here: cite-seq.com/ Although software exists, we found the exact methods very unclear so would like to present them here Many of these details have been adjusted from these discussions: github.com/Hoohm/CITE-seq-Count/issues/5 Terminology: hto: hashtag mRNA – read 2…

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Augusta University hiring Director, Bioinformatics – Immunology Center of Georgia in Augusta, Georgia, United States

About UsAugusta University is Georgia’s innovation center for education and health care, training the next generation of innovators, leaders, and healthcare providers in classrooms and clinics on four campuses in Augusta and locations across the state. More than 9,000 students choose Augusta for educational opportunities at the center of Georgia’s…

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Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues

Abstract Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and dissecting transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins, as in cells of the immune system. Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes;…

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Luecken Cite-seq human bone marrow 2021

Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and Antibody-Derived Tags (ADTs) using the 10X 3′ Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0.  File Description cite_filtered.h5mu:…

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Luecken Cite-seq human bone marrow 2021 preprocessing

Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and Antibody-Derived Tags (ADTs) using the 10X 3′ Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0.  File Description cite_quality_control.h5mu:…

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Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor

Abstract Background: The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy…

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CAMRIS hiring Bioinformatics Scientist in Bethesda, Maryland, United States

We are seeking a Bioinformatics Scientist to support the National Institutes of Health’s National Institute of Allergy and Infectious Diseases (NIAID) in support of the overall functions of the Laboratory of Allergic Diseases (LAD).   Our NIAID professional, technical, and scientific support personnel are part of a team focused on positively…

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GAP Solutions, Inc. hiring Bioinformatics Scientist in Chevy Chase, Maryland, United States

Job DescriptionPosition Objective: Provide services as a Bioinformatics Scientist in support of the overall functions of the Director of Intramural Research (DIR), Laboratory of Allergic Diseases (LAD) within the National Institute of Allergy and Infectious Diseases (NIAID).Duties And Responsibilities Provide programming and troubleshooting support to the program in the dissemination…

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How to add VDJ clonotyping data to Seurat object of scRNA-seq

How to add VDJ clonotyping data to Seurat object of scRNA-seq 0 I have performed CITE-seq (ADT, GEX, TCR) in 20 PBMC samples, consisting of responders and non-responders. By following Seurat tutorial, I performed standard pre-processing process, merging seurat object, integration, and drew the UMAP and compared the freq. of…

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COVID-19db linkage maps of cell surface proteins and transcription factors in immune cells

COVID-19db Koushul Ramjattun*, Xiaojun Ma*, Shou-Jiang Gao, Harinder Singh, Hatice Ulku Osmanbeyoglu University of Pittsburgh, UPMC Hillman Cancer Center, Center for Systems Immunology Journal of Medical Virology : onlinelibrary.wiley.com/doi/10.1002/jmv.28887 ABSTRACT The highly contagious SARS-CoV-2 and its associated disease (COVID-19) are…

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Proteomics Firm Pixelgen Targeting Fall Release of Single-Cell Spatial Analysis Tech

NEW YORK – Swedish startup Pixelgen Technologies aims to enable a new dimension of single-cell protein analysis as it launches sales of its new spatial proteomics tool. The company’s Single Cell Spatial Proteomics (SCSP) Kit allows researchers to determine both the quantity and location of 76 protein targets on the…

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Debugging Issue for CITE-seq analysis with totalVI juytper notebook tutorial – scvi-tools

Bakar June 13, 2023, 8:50pm 1 I am having issues addressing a error when trying to go through the CITE-seq analysis with totalVI notebook on my personal computer. An error surfaces when I try to run the following cell block: ————————————————————————— AttributeError Traceback (most recent call last) Cell In[9], line…

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Mapping interindividual dynamics of innate immune response at single-cell resolution

Ethical compliance This project was approved by the Wellcome Sanger Institute Animal Welfare and Ethical Review Body and complied with all relevant ethical regulations regarding animal research and human studies. Human cells were obtained from HipSci24, where they were collected from volunteers recruited from the National Institute for Health and…

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Bioinformatics Scientist job with Guidehouse

Job Family : Scientific Research & Analysis (Digital) Travel Required : None Clearance Required : Ability to Obtain Public Trust What You Will Do : Provide programming and troubleshooting support to the program in the dissemination of research data. Perform computational data analysis and data management. Work closely with staff…

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Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

Complex signaling and transcriptional programs control the development and physiology of specialized cell types. Genetic perturbations in these programs cause human cancers to arise from a diverse set of specialized cell types and developmental states. Understanding these complex systems and their potential to drive cancer is critical for the development…

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How to load inidividual ADT and RNA data to the same AnnData structure

How to load inidividual ADT and RNA data to the same AnnData structure 0 High guys, I’m a beginner using scanpy. I’m trying to load som CITE-seq data but only find how to use the “sc.read_10x_h5” function which demands a 5h file. The data I want to load is in…

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Dynamics of immune cells in the fetal brain upon viral inflammation

Research Alert Newswise — The fetal immune system undergoes many developmental milestones, with several immune cell subsets emerging during pregnancy. Recent evidence has shown that maternal infections during pregnancy can influence offspring immunity in the long term . Moreover, maternal infections are associated with an increased risk for neurodevelopmental disorders…

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Integrate and Innovate with NGS and Multiomics

Advances in genomic technologies provide researchers with access to more complete molecular datasets than ever before. Next-generation sequencing (NGS) in particular propels both basic and translational research forward, enabling scientists to see the full picture of biology. As a result, researchers now know more about the genetics and pathways underlying…

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Applications of single-cell RNA sequencing in drug discovery and development

DiMasi, J. A., Grabowski, H. G. & Hansen, R. W. Innovation in the pharmaceutical industry: new estimates of R&D costs. J. Health Econ. 47, 20–33 (2016). Article  PubMed  Google Scholar  Wouters, O. J., McKee, M. & Luyten, J. Estimated research and development investment needed to bring a new medicine to…

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Postdoctoral Fellow position in Computational Biology / Bioinformatics

Ledig stilling på Universitetet i Oslo Blindern og Urbygningen (Foto: Wikimedia og Colourbox) Deadline: 22.05.2023 Universitetet i Oslo The University of Oslo is Norway’s oldest and highest ranked educational and research institution, with 28 000 students and 7000 employees. With its broad range of academic disciplines and internationally recognised research…

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Bioconductor – Bioconductor 3.17 Released

Home Bioconductor 3.17 Released April 26, 2023 Bioconductors: We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books. There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows,…

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Singapore Researchers Develop Single-Cell Method Offering Data on Secreted Proteins, RNA

NEW YORK – A new single-cell sequencing-based method offers a way to capture data on proteins secreted by cells, such as cytokines, as well as corresponding transcriptome data. Time-resolved assessment of single-cell protein secretion with sequencing (TRAPS-seq), developed by researchers at the National University of Singapore, uses antibodies to capture…

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Sex Differences in Coronary Artery Disease and Diabetes Revealed by scRNA-Seq and CITE-Seq of Human CD4+ T Cells.

Author List Saigusa R, Vallejo J, Gulati R, Suthahar SSA, Suryawanshi V, Alimadadi A, Makings J, Durant CP, Freuchet A, Roy P, Ghosheh Y, Pandori W, Pattarabanjird T, Drago F, Taylor A, McNamara CA, Shemesh A, Lanier LL, Hedrick CC, Ley K Publication ID (Profile URL) researcherprofiles.org/profile/366106360 Publication Title Saigusa…

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PBMC CITE-seq reference | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.7779017 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7779017.svg)](https://doi.org/10.5281/zenodo.7779017) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.7779017.svg :target: doi.org/10.5281/zenodo.7779017 HTML <a href=”https://doi.org/10.5281/zenodo.7779017″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.7779017.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.7779017.svg Target URL doi.org/10.5281/zenodo.7779017 Read more here: Source link

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Bioconductor – scviR (development version)

DOI: 10.18129/B9.bioc.scviR   This is the development version of scviR; to use it, please install the devel version of Bioconductor. experimental inferface from R to scvi-tools Bioconductor version: Development (3.17) This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another…

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using CITE-seq data to cluster single cells

using CITE-seq data to cluster single cells 0 Hello, I am trying to cluster single cells using the ADT reads from the CITEseq (generated with the 10x platform). Ideally, I would like to use the information from two ADT features. I have tried the kmeans function on a count matrix…

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Enhancing Single-Cell Data & Cell Recovery Rates for Complex Tissue Samples

Broadcast Date: April 14, 2023Time: 8:00 am PT, 11:00 am ET, 17:00 CET In recent years, single-cell RNA sequencing has transformed our understanding of cellular heterogeneity within highly complex tissues and organs, revealing thus far undiscovered cell types and states and characterizing perturbations in disease. However, despite the advances in single-cell technologies,…

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Spatial and Single-Cell Computational Biology for Precision Oncology at European Molecular Biology Laboratory (EMBL)

About the team/job EMBL is Europe’s flagship laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and service teams covering the spectrum of molecular biology. It operates across six sites in Heidelberg (headquarters), Barcelona, Cambridge, Grenoble, Hamburg and Rome. Our mission is to…

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Team co-maps proteins and transcriptome in human tissues

Spatial-CITE-seq workflow design and application to diverse mouse tissue types and human tonsil for co-mapping of proteins and whole transcriptome. a, Scheme of spatial-CITE-seq. A cocktail of ADTs is applied to a PFA-fixed tissue section to label a panel of ~200–300 protein markers in situ. Next, a set of DNA…

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Gates Grubstake Fund Awards Over $1.5 Million to Campus Researchers

The Gates Grubstake Fund invokes the memory of Gold Rush prospectors who received seed money, “grubstakes,” for food and supplies so they could search for treasure. The funding supports the work of modern-day prospectors – translational researchers affiliated with Gates Institute – whose work developing cell- and gene-based therapies could…

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Comparing steps of Scanpy for scRNQ-seq and totalvi for CITE-seq – scvi-tools

Hi I have spent a few days to learn how totalvi analyze CITE-seq data and I am bit confused by the contrasting steps between Scanpy and totalvi: I have used Scanpy for 10x scRNA-seq for over 2 years now and I love it.The typical steps are as follows: Read in…

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What controls splicing to switch from CD45RA to CD45RO isoforms ?

What controls splicing to switch from CD45RA to CD45RO isoforms ? 0 Protein CD45 has many isoforms in particular CD45RA and CD45RO. It is known: Naive T lymphocytes are typically positive for CD45RA, which includes only the A protein region. Activated and memory T lymphocytes express CD45RO, the shortest CD45…

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Understanding “drop-out” for scRNA-seq data

Understanding “drop-out” for scRNA-seq data 1 “Dropout” for single cell RNA sequencing data is phenomena that some genes which are biologically expressed may nevertheless NOT be observed by the scRNA-seq procedure – i.e. if you get zero – that does not mean that it is really (biologically) zero. How should…

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Fixation Before Dissociation Using a Deep Eutectic Solvent Preserves In Vivo States and Phospho-Signalling in Single-Cell Sequencing Presented

Researchers at the University of Alabama at Birmingham have demonstrated a novel way of fixing cells and preserving their biomolecules prior to single cell dissociation without the need for harsh enzymatic/mechanical approaches. Single-cell RNA sequencing has the opportunity to deconstruct cellular networks but was previously limited by the loss of…

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BdLT-Seq as a barcode decay-based method to unravel lineage-linked transcriptome plasticity

Cell lines Immortalised HA1E (hTERT and SV40ER) and tumourigenic HA1ER cells (hTERT, SV40ER and HRAS-G12V) from stepwise tumourigenesis models generated from normal human embryonic kidney cells were obtained from Dr. Hahn (Broad Institute of MIT and Harvard, Cambridge, USA). Cells were cultured in DMEM (1 g/L glucose) (Gibco, cat. #10567014) supplemented…

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LatchBio – Bioinformatics Engineer

About Us  The convergence of laboratory automation, high-throughput assays, and machine learning is moving the medium of biological discovery to silicon. At LatchBio, we are building a ubiquitous cloud platform to store, visualize and analyze data from biological experiments. Over fifty biotech companies are using our platform to accelerate their…

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Biological reason for correlation of CD36 with S100A4 , S100A6

Biological reason for correlation of CD36 with S100A4 , S100A6 0 We are analysing single cell RNA+proteom (CITE-seq) data. One of the things we see – quite stable correlation between CD36 (protein) and S100A4 , S100A6 (rna). Question: Any ideas/comments what might be the biological reason for such correlation ?…

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The Phenotype and Function of CD26+ And CD161+ T Lymphocytes in Splenic Marginal Zone Lymphomas

Regulatory T-cells (Tregs) play a crucial role in maintaining immunological balance and regulating the body’s response to tumors in lymphoma patients. However, research on the role of Tregs in the biology and prognosis of splenic marginal zone lymphoma (SMZL) is lacking. CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing),…

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How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)

How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger) 0 Hello all. I am trying to pre-process some single cell RNA and ADT (Totalseq-C) data from an GEO SRA, but having some issues getting separate fastq’s for the “CITE-seq” (ADT)…

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Broad Institute Study Evaluates Ultima Genomics Sequencer for Single-Cell RNA-Seq

NEW YORK – Results from single-cell RNA sequencing libraries run on the new Ultima Genomics UG100 are “very similar” to those produced on Illumina’s NovaSeq, a new study says. However, the platform shows bias against 3′ gene expression libraries. Led by researchers from the Broad Institute as part of a…

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Dean’s Research Fellowship, Bioinformatics, Systems Immunology and Metabolism job with UNIVERSITY OF SURREY

Biochemical Sciences Location: Guildford Salary: £42,149 to £48,836 per annum Fixed Term for 4 years Post Type: Full Time Closing Date: 23.59 hours BST on Sunday 31 July 2022 Reference: 072121-R-R-R We are excited to invite applications for a four-year Dean’s Research Fellowship in the School of Biosciences (Faculty of Health and Medical Sciences)…

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Swarm immunology: harnessing blockchain technology and artificial intelligence in human immunology

Human immunology may soon benefit from the use of artificial intelligence and blockchain technologies. Here, we discuss how Swarm Learning could foster collaborative worldwide immunology studies that fully respect local data privacy regulations by sharing insights, not data. For decades, immunological research has benefited from highly standardized animal models. Yet,…

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Data Scientist II

Data Scientist II Overview Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the…

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Datasets – scvi-tools

data.pbmc_seurat_v4_cite_seq Dataset of PBMCs measured with CITE-seq (161764 cells). data.spleen_lymph_cite_seq Immune cells from the murine spleen and lymph nodes [GayosoSteier21]. data.heart_cell_atlas_subsampled Combined single cell and single nuclei RNA-Seq data of 485K cardiac cells with annotations. data.pbmcs_10x_cite_seq Filtered PBMCs from 10x Genomics profiled with RNA and protein. data.purified_pbmc_dataset Purified PBMC dataset…

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Postdoctoral Fellow (Bioinformatics) – Jos Melenhorst Lab

Highly motivated individuals with a PhD or MD/PhD in relevant area are encouraged to apply. This training position, under the direct supervision of a Cleveland Clinic Principal Investigator will provide practical training and experience in a research setting. This position is appointed through the Lerner Research Institute. The successful applicant…

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SCHNAPPs – Single Cell sHiNy APPlication(s)

Abstract : Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed…

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Generation of Centered Log-RatioCentered log-ratio (CLR) Normalized Antibody-Derived TagAntibody-derived tag (ADT) Counts from Large Single-Cell Sequencing Datasets

Recent developments in single-cell analysis has provided the ability to assay >50 surface-level proteins by combining oligo-conjugated antibodies with sequencing technology. These methods, such as CITE-seq and REAP-seq, have added another modality  …more Recent developments in single-cell analysis has provided the ability to assay >50 surface-level proteins by combining oligo-conjugated…

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Precision Oncology – Data Scientist – Principal Scientist, Immuno-Oncology Bioinformatics at Sanofi

  Position Overview: We seek an experienced computational biologist / data scientist to identify and advance new immuno-oncology therapies for solid tumors and hematological malignancies. In this hands-on role, you will work as an integral part of project teams to identify targets, advance programs, and develop and test actionable biomarker strategies for…

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Cell Type Prediction – covering 45 immune cell types

Tool:Cell Type Prediction – covering 45 immune cell types 0 Dear Colleagues, We just released a new tool for predicting cell types from single-cell RNA-seq data (and scRNA-seq + CITE-Seq). Currently, it covers 45 sub-types of immune cells. More subtypes are continuously being added. This tool is available in both…

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WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data

WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data 0 I want to build a UMAP from CITE-seq data with a joint embedding of the scRNA-seq and protein ab data. What’s the ‘best’ method in terms of representing the most accurate embedding? In the totalVI paper, they say totalVI >…

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