Single cell and spatial transcriptomics
Getting started guides
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A guide to single-cell transcriptomics with Oxford Nanopore
This guide introduces the single-cell RNA nanopore sequencing workflow, for ultra-rich data without compromise.
Workflow overviews
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Obtaining full-length isoforms from single cells with Oxford Nanopore sequencing
This end-to-end workflow provides a simple solution for single-cell transcriptome analysis from 10x Genomics cDNA with library preparation in approximately three hours.
Most viewed
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Alternative transcript isoform detection with single cell and spatial resolution
This application note demonstrates that Oxford Nanopore Technologies, with 10x Genomics cDNA preparation, is a reliable platform to accurately detect alternative transcript isoforms.
Featured resources
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Unlocking RNA biology with full-length reads
Discover how nanopore sequencing uniquely captures full-length transcripts for isoform-level transcriptome characterisation.
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How do I analyse my Oxford Nanopore sequencing data without specialist training?
In this beginner-friendly masterclass, discover how to analyse your Oxford Nanopore sequencing data. Find out how basecalling works, the common file formats you’ll encounter, and how to use MinKNOW to set up and monitor your sequencing run. Then, discover how to analyse your data with EPI2ME — no pr
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Which library prep workflow is right for my experiment?
Whether you’re sequencing DNA, RNA, or cDNA, a single sample or many in multiplex, there’s an Oxford Nanopore library prep kit for you. In this masterclass, discover how to choose the right one for your workflow. In this masterclass, discover: • The range of Oxford Nanopore library prep solutions av
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How do I get started with Oxford Nanopore sequencing?
Your Oxford Nanopore sequencing journey starts here. In this masterclass, find out how nanopore sequencing works, what to expect at each step of your workflow, and how to plan your first experiment. In this masterclass, discover: • How Oxford Nanopore sequencing technology works and its benefits for
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How do I load a PromethION Flow Cell?
Preparing and loading a PromethION Flow Cell is straightforward. In this demo, we walk you through the process step by step. In this masterclass, discover: • How real-time Oxford Nanopore sequencing produces data • How to use MinKNOW to monitor your sequencing run, basecall your data, and perform re
Protocols
Secuenciación transcriptómica de células individuales a partir de ADNc 3′ preparado con 10x Genomics y los kits SQK-LSK114 y EXP-PCA001
This is a single-cell transcriptomics method.
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Secuenciación transcriptómica de células individuales a partir de ADNc 5′ preparado con 10x Genomics y el kit SQK-LSK114
Learn how to sequence full‑length 5′ cDNA transcripts from 10x Genomics single‑cell assays using the Oxford Nanopore Ligation Sequencing Kit V14 (SQK‑LSK114). This high‑output method enables detailed isoform analysis, alternative splicing detection, SNP resolution, and single‑cell subtype identifica
Spatial transcriptomics sequencing from 3’ cDNA prepared with 10x Genomics using SQK-LSK114 and EXP-PCA001
This is a 10X Genomics Visium Spatial transcriptomics method.
Analysis workflows
wf-single-cell
This workflow extracts cell barcodes and UMIs from 10x-generated single cell libraries. It was initially created as a Nextflow port of Sockeye.
Latest research
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Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics
Publication: Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics
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Long-read spatial transcriptomics of patient-derived clear cell renal cell carcinoma organoids identifies heterogeneity and transcriptional remodelling following NUC-7738 treatment
Publication: Long-read spatial transcriptomics of patient-derived clear cell renal cell carcinoma organoids identifies heterogeneity and transcriptional remodelling following NUC-7738 treatment
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Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq
Publication: Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq
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Single-cell long-read whole-genome sequencing reveals somatic transposon activity in human brain
Publication: Single-cell long-read whole-genome sequencing reveals somatic transposon activity in human brain
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A complete diploid human genome benchmark for personalised genomics
Publication: A complete diploid human genome benchmark for personalised genomics
