Libraries of Restriction Fragments that Contain Replication Initiation Sites (Bubbles) Bubble-Seq prepares libraries of restriction fragments that contained replication initiation sites (bubbles) in vivo (Mesner et al., 2013). In this method, DNA from origin libraries is biotinylated by a 3ê-end tailing reaction with biotin-16-dUTP. The […]

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 […]

Microwell displacement amplification system/Immunomagnetic Separation for Targeted Bacterial Enrichment for MDA/Digital Droplet MDA Several variations on the original MDA methodã (Dean et al., 2001) such as MIDAS (Gole et al., 2013), ddMDA (Rhee et al., 2016), SNES (Leung et al., 2015), and IMS-MDA (Seth-Smith et […]

Multiple Displacement Amplification MDA is a method commonly used for sequencing microbial genomes due to its ability to amplify templates larger than 0.5 Mbp, but it can also be used to study genomes of other sizes (Dean et al., 2001). In this method, 3ê-blocked random […]

Multiple Annealing and Looping_Based Amplification Cycles MALBAC is intended to address some of the shortcomings of MDA (Zong et al., 2012). In this method, MALBAC primers randomly anneal to a DNA template. A polymerase with displacement activity at elevated temperatures amplifies the template, generating –semiamplicons.” […]

Genome and Transcriptome Sequencing G&T-seq can separate and sequence gDNA 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 beads. […]

DNA-mRNA Sequencing DR-Seq studies the genomic and transcriptomic relationship in single cells (Dey et al., 2015). Nucleic acid amplification prior to physical separation reduces sample loss and the risk of contamination. DR-Seq involves multiple amplification steps, including a quasilinear amplification technique similar to MALBAC.First, mRNA […]

Polymerase Usage Sequencing Pu-seq provides direct replication-origin location and efficiency data, as well as indirect estimates of replication timing (Daigaku et al., 2015). Alkali treatment of duplex ribonucleotide-containing DNA results in phosphate-backbone cleavage 3ê to the ribose, resulting in a 5ê-hydroxyl end. If the denatured […]

DNase l Hypersensitive Sites Sequencing DNase I footprinting was first published in 1978 (Galas et al., 1978) and predates both Sanger sequencing and NGS. The first published use with NGS was published by Boyle et al. 2008 (Boyle et al., 2008) and later optimized for […]

Linear Amplification-Mediated High-Throughput Genome-Wide Sequencing LAM-HTGTS is a method for the genome-wide detection of –prey” DSBs via their translocation to a fixed –bait” DSB in cultured mammalian cells (Hu et al., 2016). Bait-prey junctions are cloned directly from isolated gDNA using LAM-PCR and ligated unidirectionally […]