Selective 2ê-Hydroxyl Acylation Analyzed by Primer Extension Sequencing SHAPE-Seq provides structural information about RNA (Lucks et al., 2011) (Watters et al., 2016). In this method, a unique barcode is first added to the 3′ end of RNA, and the RNA is allowed to fold under […]

Selective 2ê-Hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling SHAPE-MaP sequences secondary RNA structures at various levels on a massively parallel scale. The method can be customized to interrogate small RNAs, amplicons, or rare RNA species accurately in a mixture of RNAs (Siegfried et […]

In Vivo Click Selective 2ê-Hydroxyl Acylation and Profiling Experiment icSHAPE provides accurate predictions of RNA-protein interactions and m6A modification in vivo by combining SHAPE-Seq with click chemistry for enhanced isolation (Spitale et al., 2015) (Flynn et al., 2016). , Secondary RNA structures are modified by […]

Chemical Inference of RNA Structures CIRS-Seq was developed to investigate the complexity of secondary RNA structures in the mammalian transcriptome (Incarnato et al., 2014). CIRS-Seq uses DMS to methylate the N1 of adenosine and N3 of cytosine residues, and CMC to modify pseudouridines selectively, but […]

Identification of T-Cell Receptor (TCR) a-b Chain Pairing in Single Cells This method identifies TCR-alpha and -beta chain pairing in single cells using cell-based emulsion technology for isolation, followed by NGS (Turchaninova et al., 2013). TCR chain pairing resolves one of the biggest challenges of […]

Fixed and Recovered Intact Single-Cell RNA FRISCR characterizes transcriptome profiles from fixed and stained single cells (Thomsen et al., 2016). The method uses a combination of molecular barcodes and Tn5 tagmentation to identify each cDNA fragment uniquely from every cell.The cell suspension is fixed with […]

Nuc-Seq with EdU-Mediated Labeling of Proliferating Cells Div-Seq is a single-nucleus RNA sequencing technique that improves upon Nuc-Seq by incorporating 5-ethynyl-2ê-deoxyuridine (EdU) labeling to identify dividing cells during their different cell stages (Habib et al., 2016). EdU labeling also enables identification of different cell types […]

Repertoire Sequencing / DNA Sequencing of Immunoglobulin Genes / Molecular Amplification fingerprinting Rep-Seq is a collective term for repertoire sequencing technologies (Benichou et al., 2012), including Ig-seq (Georgiou et al., 2014) and MAF (Khan et al., 2016). Ig-seq is a targeted gDNA amplification method performed […]

Nascent Strand Sequencing NS-Seq sequences nascent DNA strands to locate DNA replication origins in the genome. NS-Seq uses _-exo to digest parental DNA effectively while leaving the RNA primer_protected nascent strands intact. However, _-exo inefficiently digests G-quadruplex structures (G4) and GC-rich motifs; this bias can […]

Nascent Strand Capture and Release NSCR isolates and sequences the origin of DNA replication by capturing short nascent strands (SNS), which are single-stranded RNA-DNA chimeras (Kunnev et al., 2015). In short, NSCR captures and purifies RNA-DNA chimeric SNS, and releases the DNA part by cutting […]