All of the Low-Level RNA-Seq methods are collected together under this heading

All of the RNA-Seq sequencing methods are collected together under this heading

Transposon Sequencing or Insertion Sequencing Tn-seq (van Opijnen et al., 2009) and INSeq (Goodman et al., 2009) are nearly identical methods that determine quantitative genetic interactions accurately. INSeq includes a polyacrylamide gel purification step following adapter ligation and PCR, whereas Tn_seq requires agarose gel purification […]

Translocation-Capture Sequencing TC-Seq was developed to study chromosomal rearrangements and translocations (Klein et al., 2011). In this method, cells are infected with retrovirus expressing l-Scel sites in cells with and without activation-induced cytidine deaminase (AICDA or AID) protein. gDNA from cells is sonicated, linker-ligated, purified, […]

Specific Locus Amplified Fragment Sequencing SLAF-seq is an optimized version of ddRADseq, specifically intended for large-scale genotyping experiments (Sun et al., 2013). The enzymes and the sizes of the restriction fragments are optimized with training data to ensure even distribution and avoid repeats. The fragments […]

Nascent DNA Replication Strand Sequencing Repli-Seq maps the sequences of nascent DNA replication strands throughout the whole genome during each of the 6 cell-cycle phases (Hansen et al., 2010). This process is achieved by growing cells in media containing BrdU to replace thymidine. The cells […]

Retrotransposon Capture Sequencing RC-seq is a high-throughput protocol to map and study retrotransposon insertions (Baillie et al., 2011). In this method, after gDNA is fractionated, retrotransposon binding sites on DNA hybridize to transposon binding sites on a microarray. Deep sequencing provides accurate information that can […]

Restriction-Site Associated DNA Capture Rapture is a massively parallel, targeted DNA sequencing technique that combines RAD-seq and sequence capture to compare multiple genes of interest among large numbers of samples (Ali et al., 2016). The targeted sequencing is based on identifying restriction enzyme sites specifically […]

Restriction-Site Associated DNA Sequencing RAD-seq is a protocol for genotyping and discovery of single-nucleotide polymorphisms (SNPs) (Baird et al., 2008). This approach is particularly useful for genotyping when a reference genome is not available, such as in ecological studies (Andrews et al., 2016). PE RAD-seq, […]

Hybridization RAD for Degraded DNA hyRAD (Suchan et al., 2016) was developed for use on degraded DNA samples, such as those from museum collections. Museum and preserved samples offer a rich source of valuable specimens, but their degraded DNA is unable to sustain the double-digestion […]