Massively-parallel single nucleus RNA-seq with DroNc-seq

By Naomi Habib, I. Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R. Choudhury, F. Aguet, Ellen T. Gelfand, Kristin G. Ardlie and 4 more. Nature Methods, 2017

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Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/789deb7c1761ade9790f4ce05e1434a5e383f0d9

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Citations in the corpus

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution (2020, neutral): “Recent advances in single-cell and multiplexed spatial analysis of tissue allow us to interrogate this complexity at unprecedented resolution (Angelo et al., 2014; Buenrostro et al., 2015; Chen et al., 2016a; Chen et al., 2016b; Du et al., 2019; Gaublomme et al., 2019; Gierahn et al., 2017; Giesen e”
A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity. (2019, background): “For comparison with normal brain cell types, two single-nuclei RNA-seq datasets of normal adult human cerebral cortex were retrieved from public repositories (Habib et al., 2017; Lake et al., 2018).”
A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation (2019, positive): “Nuclei isolation was carried out using the Nuclei Isolation Kit: Nuclei EZ Prep (Sigma, #NUC101) as described(Habib et al. 2017).”
cisTopic: cis-Regulatory topic modelling on single-cell ATAC-seq data (2019, neutral): “…S10: GSE97930, GSE97887 + Fig S11: GSE100033, GSE63137, GSE82010 , Gray et al. (2017), + Fig S12: GSE97887, GSE100033, GSE97930, Gray et al. (2017), Habib et al. (2017), Mo et al. (2017), Kozlenkov et al. (2018) + Fig S13: Omni-ATAC during an EMT-like transition in melanoma (8 samples) and…”