Tag: CITE-seq

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…

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…

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…

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…

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…

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…

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…

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,…

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…

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…

Zenodo DOI Badge DOI 10.5281/zenodo.7779017 Markdown [](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

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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 ?…

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),…

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)…

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…

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)…

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,…

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…

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…

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…

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…

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…

  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…

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…

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 >…