New methods for simultaneously quantifying protein and gene expression at the single-cell level have the power to identify cell types and to classify cell populations. analysis of cells with several LY2140023 distributor high-throughput methods, all at once. We would want to integrate RNA-seq measurements with genome sequencing, protein profiles, post-transcriptional regulation, metabolomics and lipidomics, together with the cellular localization of eachall at single-cell resolution, of course. Such complete characterization of cells at the population level would be a true treasure trove for insights into cellular physiology and pathological says. A recent LY2140023 distributor work published in has made a significant step forward toward multi-omics  by producing both transcriptomes and cell-surface protein quantifications on populations of LY2140023 distributor cells. Cytometry by sequencing The methodcalled CITE-Seq (cellular indexing of transcriptomes and epitopes by sequencing)can be seen as a composite of two main concepts for how to derive cell-surface proteomics and transcriptomics from individual cells: DNA-conjugated antibodies and single-cell RNA-seq . Detecting protein levels in individual cells is usually challenging as a result of low starting amounts and the lack of direct amplification methods common for nucleic acids. New techniques for protein profiling have been published in 2014 and earlier this year [5, 6]. The main insight for how to derive cell-surface proteomics is usually to tag Rabbit Polyclonal to DP-1 proteins with antibodies conjugated to oligonucleotides (Fig.?1). By converting the detection of a protein to an oligonucleotide, the signal can then be amplified by exploiting WatsonCCrick pairing of nucleic acids. This notion has been called cytometry by sequencing . The identity of each protein is usually encoded in the oligonucleotides, which recapitulate a large number of distinguishable proteins: a sequence of length corresponds to 4unique sequences, and therefore even a sequence of eight bases would theoretically suffice for capturing all cellular proteins. Open in a separate window Fig. 1 New methods for single-cell protein profiling. In the antibody barcoding with photocleavable DNA platform (ABCD) platform, cells are permeabilized and stained using a panel of antibodies. The tagged DNA is usually cleaved, amplified by PCR, and sequenced using Nanostring technology. The Abseq method is performed by encapsulating stained cells, tagging each cell with a unique barcode, and PCR amplifying and sequencing using Illumina LY2140023 distributor technology. The cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq) method utilizes poly(A) oligonucleotides to profile cell-surface proteins and it can be coupled with single-cell RNA-seq protocols such as LY2140023 distributor Drop-Seq and Chromium (10) Ullal et al.  first demonstrated this approach by developing the antibody barcoding with photocleavable DNA platform (ABCD; Fig.?1). The authors processed bulk samples of approximately 100 cells each, as well as samples containing individual cells, from a fine-needle aspiration and profiled over 90 proteins spanning cancer-relevant pathways. The cells are permeabilized before staining, thus enabling characterization of surface and intracellular proteins. In particular, in bypassing FACS and using only non-specialized instruments, ABCD is attractive for many clinical applications. The main constraint, however, is the lack of multiplexing of the different samples/cells, which thereby limits the handling to only a few samples at a time. More recently, the Abseq method was introduced, which utilizes custom microfluidics devices  to achieve a multiplexed version of cytometry by sequencing (Fig.?1). First, cells are incubated with a variety of antibodies conjugated with oligonucleotides encoding the protein identity, followed by encapsulation in drops and pairing with additional oligonucleotides to barcode the cells. Altogether, this method requires three individual microfluidic chips, and constitutes an impressive technical feat for single-cell proteomics. RNA-Seq and cell-surface proteomics in a drop As in Abseq, cells in the CITE-Seq method are first incubated with cell-surface antibodies conjugated with oligonucleotides encoding the protein identity. CITE-Seqs second underlying concept is the application.