Excision Circle Sequencing EC-seq allows the capture and analysis of immune locus rearrangements from whole thymic and splenic tissues(Parkinson et al., 2015) .Double-stranded cleavage at recombination signal sequence (RSS) sites, mediated by recombination-activating gene recombinase (RAG), precedes genomic deletion and end-processing by the nonhomologous end-joining […]

Cas9-Digested Whole-Genome Sequencing Digenome-seq was designed to profile genome-wide Cas9 off-target effects (Kim et al., 2015). A multiplexed version has also been published (Kim et al., 2016). It belongs to a family of methods, including HTGTS (Chiarle et al., 2011), LAM-HTGTS (Hu et al., 2016), […]

Double Digest Restriction-Site Associated DNA Marker Generation ddRADseq (Peterson et al., 2012), also called ddRAD, is a variation on the RAD sequencing protocol (Baird et al., 2008), which is used for SNP discovery and genotyping (Baird et al., 2008) (Willing et al., 2011). In this […]

Contiguity-Preserving Transposition Sequencing CPT-seq is a method for genome-wide haplotyping based on contiguity-preserving transposition (CPT) and combinatorial indexing (Amini et al., 2014) . Tn5 transposition is used to modify DNA with adapter and index sequences while preserving contiguity. After DNA dilution and compartmentalization, the transposase […]

CXXC Affinity Purification Sequencing CAP-seq maps methylated CpGs in gDNA (Illingworth et al., 2010). In this method, DNA is incubated with CXXC bound to nickel-charged sepharose beads. Next, DNA is eluted from the complex and sequenced. Deep sequencing provides insights into methylated CpG sites in […]

RAD With Type IIB Restriction Endonucleases 2b-RAD is similar to ddRadseq but uses type IIB restriction enzymes (BsaXI or AlfI), which will cleave upstream and downstream of a recognition site(Wang et al., 2012) . This shears the target genome into a large number of DNA […]

All of the Sequence Rearrangement sequencing methods are collected together under this heading

Proteomic Peptide-Phage Display / PDZ Domains Sequencing ProP-PD is a protocol that identifies short linear motif (SLiM) interactions or PDZ domains (PDZ-Seq) (Ivarsson et al., 2014) (Ernst et al., 2010). ProP-PD can be used for the direct identification of ligands with potential biological relevance. This […]

Candidate Cellular Protein Target Identification PD-Seq is a protocol to identify cellular targets for proteins through protein-protein interactions (Arango et al., 2013). In this method, researchers identified cellular targets for apigenin. They coupled apigenin to amino polyethyleneglycol-polyacrylamide copolymer (PEGA) beads after activation with 4-nitrophenyl bromoacetate. […]

All of the Protein-Protein Interaction sequencing methods are collected together under this heading