54 articles
3' rapid amplification of cDNA ends
3' rapid amplification of cDNA ends (3' RACE) is a PCR method that maps a transcript's 3' end and polyadenylation site, using one gene-specific primer and the poly(A) tail.
Bru-seq
Bru-seq is a metabolic-labeling sequencing method, introduced in 2013, that captures newly transcribed RNA by pulse-labeling living cells with bromouridine, measuring active transcription and mapping it across the genome.
Cap analysis of gene expression
Cap analysis of gene expression (CAGE) is a transcriptomics method, reported in 2003, that sequences the capped 5' ends of RNAs to map transcription start sites and quantify promoter activity.
CAT tailing
CAT tailing is a laboratory method for measuring poly(A) tail length on RNA, combining RNA circularization with tailing plus template switching to create a sequenceable tail.
CEL-seq
CEL-seq is a single-cell RNA sequencing method, introduced in 2012, that barcodes each cell's RNA during reverse transcription and amplifies transcripts linearly by in vitro transcription.
Chromatin isolation by RNA purification sequencing
Chromatin isolation by RNA purification sequencing (ChIRP-seq) is a hybridization-capture method, reported in 2011, that maps the genomic binding sites of one chosen RNA by sequencing.
CLIP-Seq
CLIP-Seq, cross-linking immunoprecipitation followed by sequencing, maps the RNA transcripts a specific RNA-binding protein contacts inside cells, down to exact nucleotides in modern variants like iCLIP and eCLIP.
Cross-linking and immunoprecipitation
Cross-linking and immunoprecipitation (CLIP) is a method for identifying the RNA targets of RNA-binding proteins in living cells, combining UV cross-linking with immunoprecipitation and sequencing.
De novo transcriptome assembly
De novo transcriptome assembly is a bioinformatics method that reconstructs transcript sequences directly from RNA sequencing reads without a reference genome, using tools such as Trinity.
Differential display
Differential display, also called DD-PCR or DDRT-PCR, is a PCR-based method for comparing mRNA populations between samples and isolating differentially expressed genes, introduced in 1992.
Digital spatial profiling
Digital spatial profiling (DSP) is a spatial omics method that quantifies dozens to thousands of proteins or transcripts in selected regions of tissue sections, commercialized as GeoMx and reported in 2020.
Direct RNA sequencing
Direct RNA sequencing, also known as direct RNA-seq, is a nanopore method that reads native RNA molecules single-file through a protein pore, detecting modifications like m6A.
DroNc-seq
DroNc-seq is a droplet-based single-nucleus RNA sequencing method that profiles gene expression in thousands of nuclei from frozen or archived tissue, such as post-mortem human brain.
Drop-seq
Drop-seq is a droplet microfluidic single-cell RNA sequencing method introduced in 2015 that co-encapsulates cells with DNA-barcoded beads in nanoliter droplets, profiling thousands of cells at a cost of pennies per cell.
Dual RNA-seq
Dual RNA-seq is a transcriptomics method that simultaneously sequences host and pathogen RNA from one infected sample, separating the two transcriptomes computationally rather than physically.
eCLIP
eCLIP, or enhanced crosslinking and immunoprecipitation, is a molecular biology method mapping RNA-binding protein contacts transcriptome-wide at single-nucleotide resolution, introduced by Van Nostrand in 2016.
Expansion sequencing
Expansion sequencing (ExSeq) is an imaging method that physically expands preserved tissue in a swellable hydrogel before in situ sequencing, mapping RNA transcripts at nanoscale resolution.
Footprinting
Footprinting is a bench technique for locating protein-binding sites on DNA or RNA, where a bound protein shields its site from cleavage; Galas and Schmitz first reported it in 1978.
Full-length cDNA sequencing
Full-length cDNA sequencing is a transcriptomic method that copies complete messenger RNA molecules into DNA and sequences each end to end, revealing isoforms, splice sites, and gene fusions.
Full-length transcriptome sequencing
Full-length transcriptome sequencing reads entire RNA transcript molecules end to end on long-read platforms such as PacBio Iso-Seq and Oxford Nanopore, determining complete isoform sequences directly.
Gene expression profiling
Gene expression profiling, also known as expression profiling, is a molecular biology method that measures mRNA levels of many genes at once, using microarrays or RNA sequencing.
iCLIP
iCLIP is a molecular biology method that maps where an RNA-binding protein contacts RNA inside cells, using UV crosslinking and sequencing to resolve each crosslink site to a single nucleotide.
Isoform sequencing
Isoform sequencing (ISO-seq) is a long-read sequencing method that reads full-length RNA transcripts, from the poly(A) tail to the end, identifying complete splice isoforms without assembly.
miRNA microarray analysis
miRNA microarray analysis is a hybridization-based method that measures microRNA abundance in cells or tissues using fluorescently labeled miRNAs and thousands of immobilized complementary probes.
Northern blot
The Northern blot is a molecular biology technique that separates RNA by gel electrophoresis and detects a chosen sequence with a labeled probe, reporting a transcript's size and abundance.
Nuclease protection assay
The nuclease protection assay (NPA) is a molecular biology method that quantifies and maps specific RNA or DNA using a labeled antisense probe and nuclease digestion.
PAR-CLIP
PAR-CLIP is a molecular biology method that maps RNA-binding protein binding sites across the transcriptome at single-nucleotide resolution, introduced by Markus Hafner and colleagues in 2010.
Parallel analysis of RNA structure (PARS)
Parallel analysis of RNA structure (PARS) is a high-throughput sequencing method measuring RNA secondary structure transcriptome-wide, introduced by Michael Kertesz and colleagues in Nature in 2010.
Poly(A)-site sequencing
Poly(A)-site sequencing (PAS-seq) is a deep-sequencing method that maps polyadenylation sites across a transcriptome and quantifies RNA abundance, introduced by Peter J. Shepard and colleagues in 2011.
Precision nuclear run-on sequencing
Precision nuclear run-on sequencing (PRO-seq) is a molecular biology method that maps engaged RNA polymerases genome-wide at base-pair resolution by sequencing the 3' ends of nascent RNA, detecting enhancers and direct transcriptional changes.