Single-Molecule Molecular Inversion Probes The smMIP method uses single-molecule tagging and molecular inversion probes to detect and quantify genetic variations occurring at low frequencies (Hiatt et al., 2013). In this method, probes are used to detect targets in gDNA. After the probed targets are copied, […]

Single-Molecule Droplet Barcoding SMDB is a method to leverage short-read sequencing to obtain long and accurate reads (Lan et al., 2016). Using a microfluidics system, the method isolates, amplifies, fragments, and barcodes single DNA molecules in aqueous picoliter droplets. This approach allows the full-length molecules […]

Single-Cell Retrotransposon Capture Sequencing Single-cell RC-seq uses sequence capture to enrich DNA for the junctions between retrotransposon termini and adjacent genomic regions, followed by paired-end sequencing (Upton et al., 2015). In this method, nuclei are purified first by fluorescence-activated cell sorting (FACS) and then picked […]

Single-Cell Methylome and Transcriptome Sequencing scM&T-seq allows parallel analysis of both epigenetic and gene expression patterns from single cells using Smart-seq2 and scBS-seq (Angermueller et al., 2016). scM&T-Seq is based on G&T-seq, but instead of using MDA for DNA sequencing, it uses scBS-Seq to determine […]

Single-Cell Bisulfite Sequencing scBS-seq is a version of the well-established bisulfite sequencing (BS-seq) and post-bisulfite adapter tagging (PBAT) protocols, modified to detect methylated cytosines in gDNA from single cells (Smallwood et al., 2014). In this method, after single cells are isolated, gDNA is treated with […]

Single-Cell Assay for Transposase-Accessible Chromatin This version of scATAC-seq is integrated into a programmable microfluidics platform (Buenrostro et al., 2015). The method is similar to scATAC-seq (combinatorial indexing version), which relies on indexing to identify single cells (Cusanovich et al., 2015). In this protocol the […]

Single-Cell Assay for Transposase-Accessible Chromatin This version of scATAC-seq uses combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay. This method avoids the need for compartmentalization of individual cells, which makes the system scalable to analyze thousands of cells at […]

Detect 5hmC Marks in Single Cells With AbaSI Nuclease scAba-seq is a single-cell, genome-wide, and strand-specific 5hmC sequencing technology (Mooijman et al., 2016). 5hmC marks in DNA from individual cells are glucosylated with T4 phage _-glucosyltransferase (T4-_GT_, and the DNA is digested with the restriction […]

Safe-Sequencing System is a Unique Molecular Identifier (UMI) Approach to Detect Rare Variants Safe-SeqS (or, more commonly, Safe-Seq) is an approach that uses unique molecular identifiers (UMIs) to detect rare variants (Kinde et al., 2011). In the time after the publication of the method in […]

Oligonucleotide-Selective Sequencing OS-Seq was developed to improve targeted resequencing by capturing and sequencing gene targets directly on the flow cell (Myllykangas et al., 2011). In this method, target sequences with adapters are used to modify the flow cell primers. Targets in the template are captured […]