Single G2/M Nucleus Sequencing of Cells in S Phase/Single Nucleus Exome Sequencing A modified MDA protocol, nuc-seq takes advantage of the fact that a single cell in the G2_M stage of the cell cycle has 4 copies of the genome. This property allows the cells […]

Targeted Capture of STR Loci by smMIPs MIPSTR is a method for multiplex genotyping of germline and somatic short tandem repeat (STR) variation across many individuals (Carlson et al., 2015). This method is a variation of the smMIP (Hiatt et al., 2013) approach and uses […]

Duplex Sequencing Duplex-Seq is a tag-based, error-correction method to improve sequencing accuracy (Schmitt et al., 2012). In this method, adapters (with primer sequences and random 12 bp indexes) are ligated onto the template and amplified using PCR. Deep sequencing provides consensus sequence information from every […]

Droplet-Based Single-Cell Chromatin Immunoprecipitation Sequencing Drop-ChIP or scChIP-seq analyzes the chromatin states of single cells by using microfluidics, unique molecular barcodes, and NGS (Rotem et al., 2015). In this method, single cells are isolated into droplets containing lysis buffer and micrococcal nuclease (MNase), and then […]

All of the Low-Level DNA Detection methods are collected together under this heading

Tagmentation-Based Whole-Genome Bisulfite Sequencing T-WGBS uses the Tn5 transposome and bisulfite conversion to study 5mC (Wang et al., 2013). In this method, DNA is incubated with Tn5 transposome containing methylated primers, which fragments the DNA and ligates adapters. The tagged DNA first undergoes oligonucleotide displacement, […]

Tet-Assisted 5-Methylcytosine Sequencing TAmC-Seq selectively tags 5mC with an azide residue that can be further labeled with biotin for affinity purification (Zhang et al., 2013). The method relies on the properties of the Ten-eleven translocation (Tet) family of iron(II)/α-ketoglutarate-dependent dioxygenases that are involved in the […]

Tet-Assisted Bisulfite Sequencing TAB-Seq is a novel method that uses bisulfite conversion and Tet proteins to study 5hmC (Yu et al., 2012). In this method, 5hmC is first protected selectively with a glucose moiety, followed by subsequent oxidation of 5mC to 5caC by Tet proteins. […]

Reduced-Representation M.SssI Methylase-Assisted Bisulfite Sequencing RRMAB-seq is based on the pretreatment of gDNA with the enzyme MspI, which recognizes and cuts the CCGG consensus to enrich CpG-rich regions, like gene promoters (Neri et al., 2015). This method is an adapted version of MAB-seq (Wu et […]

Reduced-Representation Bisulfite Sequencing RRBS uses one or multiple restriction enzymes on the genomic DNA to produce sequence-specific fragmentation (Meissner et al., 2005). The fragmented genomic DNA is treated with bisulfite and sequenced. This is the method of choice to study specific regions of interest. It […]