New Genomics Method Enables Large-Scale Multidimensional Single Cells Analysis

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CITE-seq, or Cellular Indexing of Transcriptomes and Epitopes by sequencing, couples the measurement of surface protein markers on thousands of single cells with simultaneous sequencing of the messenger RNA (mRNA or transcriptomes) of those same single cells.

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The NYGC researchers’ proof-of-concept study of CITE-seq, published in Nature Methods, monitored 10 surface proteins, together with transcriptomes, of 8,000 single cells, the largest scale demonstration of multidimensional single-cell analysis to date.

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“No other method allows simultaneous measurements of transcriptomes and proteins on the same scale,” said Marlon Stoeckius, PhD, a Research Scientist in the NYGC’s Technology Innovation Lab, who led CITE-seq’s development. “CITE-seq adds to already established methods for transcriptome analysis without any detrimental effects on the quality of the data generated.”

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The protein detection component of CITE-seq is based on DNA-barcoded antibodies, which produce a sequenceable readout that is captured along with the transcriptome of the cell. The integration of the protein and RNA data generated by CITE-seq required custom data analysis, which was developed in close collaboration with the lab of Rahul Satija, PhD, a Core Faculty Member at the NYGC. As an example of the power of CITE-seq, the investigators used the multimodal data to identify subclasses of natural killer (NK) cells that are difficult to distinguish based on transcriptomes alone.

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The capacity of CITE-seq to more finely dissect cell populations has many potential applications in clinical research. “One possible future direction is to use CITE-seq on tumour samples to examine both individual tumour cells and the different pools of immune cells that infiltrate the tumour. This approach could be very useful in the deep characterization of tumour heterogeneity and in the development of new immunotherapeutic approaches,” Dr. Stoeckius said.

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News Reference: New Genomics Tool CITE-Seq Enables Large-Scale Multidimensional Analysis of Single Cells

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