High-Throughput Single-Cell Labeling with Indexing Droplets inDrop is used for high-throughput single-cell labeling (Klein et al., 2015). This approach is similar to Drop-seq, but it uses hydrogel microspheres to introduce the oligonucleotides.Single cells from a cell suspension are isolated into droplets containing lysis buffer. After […]

High-Throughput Single-Cell Labeling Hi-SCL generates transcriptome profiles for thousands of single cells using a custom microfluidics system, similar to Drop-Seq and inDrop (Rotem et al., 2015). Single cells from cell suspension are isolated into droplets containing lysis buffer. After cell lysis, cell droplets are fused […]

Genome and Transcriptome Sequencing G&T-Seq can separate and sequence genomic DNA and full-length mRNA from single cells (Macaulay et al., 2015). In this method, single cells are isolated and lysed. RNA is captured using biotinylated oligo(dT) capture primers and separated from DNA using streptavidin-coated magnetic […]

Analysis of mRNA Transcripts from Individual Cells in Droplets Drop-Seq analyzes mRNA transcripts from droplets of individual cells in a highly parallel fashion (Macosko et al., 2015). This single-cell sequencing method uses a microfluidic device to compartmentalize droplets containing a single cell, lysis buffer, and […]

Designed Primer_Based RNA Sequencing DP-Seq amplifies mRNA from limited starting material, as low as 50 pg (Bhargava et al., 2014). In this method, a specific set of heptamer primers is designed. The enriched poly(A)-selected mRNA undergoes first-strand cDNA synthesis. Next, the designed primers are hybridized […]

Digital RNA Sequencing Digital RNA sequencing is an approach to RNA-Seq that removes sequence-dependent PCR amplification biases by barcoding the RNA molecules before amplification (Shiroguchi et al., 2012). RNA is reverse-transcribed to cDNA, and an excess of adapters, each with a unique barcode, is added […]

Gene Expression Cytometry CytoSeq enables gene expression profiling of thousands of single cells (Fan et al., 2015). In this method, single cells are randomly deposited into wells. A combinatorial library of beads with specific capture probes is added to each well. After cell lysis, mRNAs […]

Cell Labeling via Photobleaching CLaP is a noninvasive, laser-based labeling technique for single cells (Binan et al., 2016). The method uses lasers to crosslink specific cells with fluorescent tags before isolating individual cells for sequencing.In CLaP, cells of interest are tagged by crosslinking biotin-4-fluorescein (B4F) […]

Identification of Low-Abundance RNA Viruses with Circular Sequencin CirSeq accurately identifies ultra-rare and low-frequency genetic variants in RNA viruses. The method uses a unique step for circularization of fragmented viral RNAs, followed by rolling-circle RT (Acevedo et al., 2014) (Acevedo et al., 2014). CirSeq corrects […]

Cell Expression by Linear Amplification Sequencing CEL-Seq uses barcoding and pooling of RNA to overcome challenges from low input (Hashimshony et al., 2012). In this method, each cell undergoes RT with a unique barcoded primer in its individual tube. After second-strand synthesis, cDNAs from all […]