Tag: CITE-seq

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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