AbPair is an emulsion-based method for paired sequencing of immunoglobulin (antibody) and T cell receptor (TCR) variable regions. It has been extended to expression strength quantitation for multi-gene panels, and for cell surface protein quantitation with DNA-barcoded affinity reagents. Tumor-infiltrating immune repertoires captured by single-cell […]

UV-C Crosslinking and Immunoprecipitation irCLIP maps protein-RNA interaction sites using less sample material, time, and increased cDNA library quality compared to previous CLIP methods (Zarnegar et al., 2016). irCLIP was designed to tackle the issues in both iCLIP and HITS-CLIP, such as reverse-transcriptase halting and […]

High-Throughput SequencingãRNA Affinity Profiling HiTS-RAP is a quantitative method to evaluate binding interactions of RNA aptamers with their proteins at a massive scale (Tome et al., 2014) (Ozer et al., 2015). HiTS-RAP transcribes DNA directly on the flow cell and measures the binding affinity of […]

CLIP with BrdU Affinity Purification BrdU-CLIP sequences the binding sites of RBPs with single-nucleotide resolution. BrdU-CLIP fixes a major problem in HITS-CLIP where 5′ adapters are not attached to the cDNA due to premature termination of reverse transcription (Weyn-Vanhentenryck et al., 2014). BrdU-CLIP uses BrdUTPs […]

Native Elongating Transcript Sequencing Technology for Mammalian Chromatin mNET-Seq generates profiles of nascent RNA and cotranscriptional RNA processing associated with different C-terminal domain (CTD) phosphorylation states throughout the whole genome (Nojima et al., 2015). mNET-Seq is able to provide precise sequence reads of RNAPII active […]

Genome-wide Mapping of Uncapped and Cleaved Transcripts GMUCT is a method for constructing sequencing libraries made up of decapped or cleaved mRNAs (Gregory et al., 2008). There are 2 versions of GMUCT: version 1.0 was developed in 2008, while a more streamlined and efficient version […]

Flowcell Reverse Transcription Sequencing Flow-cell surface reverse transcription sequencing (FRT-Seq) is an transcriptome sequencing technique developed in 2010 by Mamanova et al (Mamanova et al., 2010). The method is strand-specific, free of amplification, and compatible with paired-end sequencing. To begin with, poly(A) RNA samples are […]

2′,3′-cyclic phosphate (cP) RNA Sequencing 2′,3′-cyclic phosphate (cP) RNA sequencing (cP-RNA-Seq) is a method to isolate and sequence RNA species protected by cP at their 3′ terminus, which usually prevents adapter ligation (Honda et al., 2016). The researchers originally developed this technique to identify transfer […]

RNA Capture Sequencing CaptureSeq is a targeted RNA sequencing method that is able to provide higher sequencing coverage for selected regions of the genome(Mercer et al., 2014).This method follows the TruSeq RNA sample preparation protocol, in which mRNA is first isolated from total RNA by […]

4-Thiouridine and 5,6-Dichlorobenzimidazole 1-b-D-Ribofuranoside Sequencing 4sUDRB-Seq investigates initiation frequencies and RNA elongation rates throughout the genome using 4-thiouridine (4-SU) and DRB (Fuchs et al., 2014). Cells are first treated with DRB to inhibit RNA elongation and arrest RNAPII at TSS. The cells are lysed, cleansed […]