Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transcriptional Spaces

We describe a universal sample multiplexing method for single-cell RNA-seq in which cells are chemically labeled with identifying DNA oligonucleotides. Analysis of a 96-plex perturbation experiment revealed changes in cell population structure and transcriptional states that cannot be discerned from bulk measurements, establishing a cost effective means to survey cell populations from large experiments and clinical samples with the depth and resolution of single-cell RNA-seq.

• Publication year

  2018

• Venue

  bioRxiv

• Publication date

  2018-05-05

• Fields of study

  Biology

• Identifiers
  DOI 10.1101/315333
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Faculty Opinions recommendation of Simultaneous epitope and transcriptome measurement in single cells.

  2020cited by this paper
• Mapping the Mouse Cell Atlas by Microwell-Seq.

  2018cited by this paper
• Faculty Opinions recommendation of Comprehensive single-cell transcriptional profiling of a multicellular organism.

  2018cited by this paper
• Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

  2018cited by this paper
• Single-Cell Transcriptional Profiling of a Multicellular Organism

  2017cited by this paper
• Large-scale simultaneous measurement of epitopes and transcriptomes in single cells

  2017cited by this paper
• Pooled CRISPR screening with single-cell transcriptome read-out

  2017cited by this paper
• Exponential scaling of single-cell RNA-seq in the past decade

  2017cited by this paper
• Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

  2017cited by this paper
• Multiplexed quantification of proteins and transcripts in single cells

  2017cited by this paper
• Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

  2015cited by this paper
• Adult Mammalian Neural Stem Cells and Neurogenesis: Five Decades Later.

  2015cited by this paper
• Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

  2015cited by this paper
• Full-length RNA-seq from single cells using Smart-seq2

  2014cited by this paper
• Oscillatory Control of Factors Determining Multipotency and Fate in Mouse Neural Progenitors

  2013cited by this paper
• High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

  2011cited by this paper
• Mammalian Gcm genes induce Hes5 expression by active DNA demethylation and induce neural stem cells

  2011cited by this paper
• Direct cell surface modification with DNA for the capture of primary cells and the investigation of myotube formation on defined patterns.

  2009cited by this paper
• Models from experiments: combinatorial drug perturbations of cancer cells

  2008cited by this paper
• The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease

  2006cited by this paper
• A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis

  2005cited by this paper
• Fundamentals of planarian regeneration.

  2004cited by this paper

• DOT1L activity affects neural stem cell division mode and reduces differentiation and ASNS expression

  2023influential citation
• Evaluation of Computational Methods for Single Cell Multi-Omics Integration

  2023cites this paper
• Single-cell genome and transcriptome sequencing without upfront whole-genome amplification reveals cell state plasticity of melanoma subclones

  2023cites this paper
• Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution

  2022cites this paper
• Predicting single-cell perturbation responses for unseen drugs

  2022cites this paper
• Benchmarking atlas-level data integration in single-cell genomics

  2020cites this paper
• Molecular evolution of gland cell types and chemical interactions in animals

  2020cites this paper
• Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

  2020cites this paper
• CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing

  2020cites this paper
• Massively multiplex chemical transcriptomics at single-cell resolution

  2019cites this paper
• Designing signaling environments to steer transcriptional diversity in neural progenitor cell populations

  2019cites this paper
• MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

  2019cites this paper
• The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

  2019cites this paper
• Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

  2019cites this paper
• Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

  2019cites this paper
• Embracing Systems Toxicology at Single-Cell Resolution.

  2019cites this paper
• CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics

  2019cites this paper
• Ovarian cancer and the evolution of subtype classifications using transcriptional profiling†

  2019cites this paper
• Current best practices in single‐cell RNA‐seq analysis: a tutorial

  2019cites this paper
• Single-cell sequencing and its applications in head and neck cancer.

  2019cites this paper
• Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries

  2018cites this paper
• CellTag Indexing: a genetic barcode-based multiplexing tool for single-cell technologies

  2018cites this paper
• Scrublet: computational identification of cell doublets in single-cell transcriptomic data

  2018cites this paper
• Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

  2018cites this paper
• High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations

  2018cites this paper
• DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors

  2018cites this paper
• Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

  2018cites this paper
• Developmental Cell Perspective The Pediatric Cell Atlas : Defining the Growth Phase of Human Development at Single-Cell Resolution

  year unknowncites this paper