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Nature Protocols is an interactive online resource for all laboratory protocols relevant to biological and biomedical research. Nature Protocols includes a free-to-access community site, 'Protocols Network', containing protocols that are posted direc

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Preparation of single-cell suspensions of mouse glomeruli for high-throughput analysis

Nature Protocols, Published online: 19 July 2021; doi:10.1038/s41596-021-00578-2The glomerulus is a difficult-to-isolate structure that is often poorly represented in single-cell kidney preparations. This protocol describes the isolation of high-quality mouse glomerular cells for high-throughput analyses.

A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility

Nature Protocols, Published online: 19 July 2021; doi:10.1038/s41596-021-00583-5This protocol describes a plate-based ATAC-seq assay that combines up-front bulk tagging of accessible DNA by the Tn5 transposase with FACS sorting for robust and cost-efficient profiling of chromatin accessibility in single cells.

Preparation of single-cell suspensions of mouse glomeruli for high-throughput analysis

A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility

Testing physiologically relevant conditions in minimal inhibitory concentration assays

Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation

Nature Protocols, Published online: 09 July 2021; doi:10.1038/s41596-021-00566-6Mass-spectrometry-based proteomics is a powerful approach for discovering disease biomarkers. This tutorial provides advice on the study design, including cohort selection, evaluating statistical power, blinding and randomization, and quality control.

Smart-RRBS for single-cell methylome and transcriptome analysis

Nature Protocols, Published online: 09 July 2021; doi:10.1038/s41596-021-00571-9This is a protocol for profiling the methylome and transcriptome of a single cell by using Smart-seq2 and reduced representation bisulfite sequencing.

Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation

Smart-RRBS for single-cell methylome and transcriptome analysis

Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor

Nature Protocols, Published online: 07 July 2021; doi:10.1038/s41596-021-00575-5This protocol provides step-by-step instructions for using MetaNeighbor, a computational tool that allows quantification of cell-type replicability across single-cell transcriptomic datasets and identifies the gene sets that contribute to cell identity.

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