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Literature DB >> 31873215

Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins.

Jase Gehring^1,2, Jong Hwee Park², Sisi Chen², Matthew Thomson², Lior Pachter^3,4.

Abstract

We describe a universal sample multiplexing method for single-cell RNA sequencing in which fixed cells are chemically labeled by attaching identifying DNA oligonucleotides to cellular proteins. Analysis of a 96-plex perturbation experiment revealed changes in cell population structure and transcriptional states that cannot be discerned from bulk measurements, establishing an efficient method for surveying cell populations from large experiments or clinical samples with the depth and resolution of single-cell RNA sequencing.

Entities: Chemical Species

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Year: 2019 PMID： 31873215 DOI： 10.1038/s41587-019-0372-z

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

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Cited

22 in total

Review 1. Tools and Concepts for Interrogating and Defining Cellular Identity.

Authors: Kara L McKinley; David Castillo-Azofeifa; Ophir D Klein
Journal: Cell Stem Cell Date: 2020-05-07 Impact factor: 24.633

Review 2. Sample-multiplexing approaches for single-cell sequencing.

Authors: Yulong Zhang; Siwen Xu; Zebin Wen; Jinyu Gao; Shuang Li; Sherman M Weissman; Xinghua Pan
Journal: Cell Mol Life Sci Date: 2022-08-05 Impact factor: 9.207

3. Universal Surface Biotinylation: a simple, versatile and cost-effective sample multiplexing method for single-cell RNA-seq analysis.

Authors: Michihiko Sugimoto; Yuhki Tada; Shigeyuki Shichino; Saeko Koyamatsu; Noriyuki Tsumaki; Kuniya Abe
Journal: DNA Res Date: 2022-05-27 Impact factor: 4.477

4. Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition.

Authors: Johannes Bues; Marjan Biočanin; Joern Pezoldt; Riccardo Dainese; Antonius Chrisnandy; Saba Rezakhani; Wouter Saelens; Vincent Gardeux; Revant Gupta; Rita Sarkis; Julie Russeil; Yvan Saeys; Esther Amstad; Manfred Claassen; Matthias P Lutolf; Bart Deplancke
Journal: Nat Methods Date: 2022-02-14 Impact factor: 47.990

5. Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign.

Authors: Sisi Chen; Paul Rivaud; Jong H Park; Tiffany Tsou; Emeric Charles; John R Haliburton; Flavia Pichiorri; Matt Thomson
Journal: Proc Natl Acad Sci U S A Date: 2020-10-30 Impact factor: 11.205

6. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.

Authors: Eleni P Mimitou; Caleb A Lareau; Kelvin Y Chen; Andre L Zorzetto-Fernandes; Yuhan Hao; Yusuke Takeshima; Wendy Luo; Tse-Shun Huang; Bertrand Z Yeung; Efthymia Papalexi; Pratiksha I Thakore; Tatsuya Kibayashi; James Badger Wing; Mayu Hata; Rahul Satija; Kristopher L Nazor; Shimon Sakaguchi; Leif S Ludwig; Vijay G Sankaran; Aviv Regev; Peter Smibert
Journal: Nat Biotechnol Date: 2021-06-03 Impact factor: 68.164

Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins.

Review 1. Tools and Concepts for Interrogating and Defining Cellular Identity.

Review 2. Sample-multiplexing approaches for single-cell sequencing.

3. Universal Surface Biotinylation: a simple, versatile and cost-effective sample multiplexing method for single-cell RNA-seq analysis.

4. Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition.

5. Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign.

6. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.

Review 7. The Impact of Single-Cell Genomics on Adipose Tissue Research.

8. Dissociation of microdissected mouse brain tissue for artifact free single-cell RNA sequencing.

9. Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration.

10. Extrathymic Aire-expressing cells support maternal-fetal tolerance.