Experimental techniques for lncRNA annotation and profiling



Existing tools performing subcellular localization prediction

On this page, we have enlisted the popular experimental techniques that are used to investigate lncRNA biology. Most of the techniques are either based on RNA imaging or RNA profiling. Click on the headers to sort them accordingly.


Experimental methodsBrief description
smFISH smFISH (single-molecule fluorescence in situ hybridization) is a molecular biology technique that allows for the visualization and quantification of individual RNA molecules in cells or tissues.
smiFISH smiFISH (single molecule inexpensive fluorescence in situ hybridization) uses unlabelled primary probes and a fluorescently labelled secondary detector oligonucleotide, allowing to use more probes per mRNA resulting in a substantial increase in detection efficiency
SNV FISH SNV FISH (single nucleotide variant fluorescence in situ hybridization) is a molecular technique that can detect single-base changes in DNA sequences within cells or tissues, enabling the visualization and analysis of genetic variations at high resolution.
inoFISH inoFISH (inosine fluorescence in situ hybridization) can directly visualize and quantify adenosine-to-inosine edited transcripts in situ
SABER-FISH SAREFISH (Signal amplification by exchange reaction fluorescence in situ hybridization) is a molecular imaging technique that uses a hybridization-based signal amplification strategy to enhance the sensitivity of FISH, enabling the detection of low-abundance RNA targets in cells and tissues.
ClampFISH ClampFISH (click-amplifying fluorescence in situ hybridization) is a modified version of FISH with improved specificity and signal amplification
seqFISH+ seqFISH (spatially resolved transcriptomics by fluorescence in situ hybridization) is a high-throughput, multiplexed imaging technique that enables simultaneous detection of thousands of RNA molecules in situ and reconstruction of their spatial organization in tissues or cells.
MERFISH MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization) is a high-throughput, multiplexed imaging technique that can detect and localize thousands of RNA molecules simultaneously within cells or tissues, enabling highly detailed and comprehensive gene expression profiling.
STARmap STARmap combines hydrogel-tissue chemistry and in situ DNA sequencing to achieve intact-tissue single-cell measurement of expression of more than a thousand genes
HyblSS Hybridization-based in situ sequencing (HybISS) is a method that combines in situ hybridization with DNA sequencing to detect and identify RNA molecules at the single-cell level, allowing for spatially resolved transcriptomics analysis.
FISSEQ FISSEQ (Fluorescent In Situ Sequencing) is a spatial transcriptomics technique that combines FISH with next-generation sequencing to enable high-throughput, multiplexed detection of RNA molecules and their precise spatial locations within tissues, providing a comprehensive view of gene expression patterns.
RNA stem-loop system The RNA stem-loop system allows for the controlled expression of RNA molecules in cells by using a stem-loop structure to stabilize transcripts and when combined with a fluophore allows imaging
Cas system CRISPR-mediated RNA imaging technique involves the use of a modified CRISPR-Cas system that targets specific RNA molecules and recruits fluorescent proteins to them
RNA-seq RNA sequencing (RNA-Seq) uses the capabilities of high-throughput sequencing methods to provide insight into the transcriptome of a cell
Microarray Microarray RNA profiling is a technique that allows the simultaneous detection and quantification of the expression levels of thousands of RNA transcripts
Tiling arrays Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions
SAGE CAGE Serial analysis of gene expression (SAGE) was developed to analyze the transcriptome in terms of identification and quantification of transcripts, including ncRNAs. Cap analysis gene expression (CAGE), a modified verison of SAGE, involves the isolation of short sequence tags at the 5′ end of full-length mRNAs, which contrasts with SAGE where tags originate at the 3′ end of the mRNA
PARE PARE (Parallel Analysis of RNA Ends) is a high-throughput sequencing-based method used to identify and quantify small RNA molecules, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), in a given sample
degradome-seq Degradome-seq is another high-throughput sequencing-based method used to study RNA molecules, but it focuses on identifying the specific cleavage sites of endonucleases, such as miRNA-guided endonucleases, on target RNAs.
GRO-seq GRO-seq (Global Run-On sequencing) is a method used to study transcriptional activity of the genome at a global scale.
RIP, CUP RIP (RNA immunoprecipitation) and CUP (crosslinking and immunoprecipitation) are two related methods used to study the interactions between RNA molecules and RNA-binding proteins (RBPs).
TIF-seq TIF-seq (transcription initiation footprinting and sequencing) is a sequencing-based method used to study the initiation of transcription in a genome-wide manner.
Selective 2'-hydroxyl acylation by primer extension (SHAPE) Selective 2'-hydroxyl acylation by primer extension (SHAPE) is a chemical probing technique used to study RNA structure and folding.
PARS PARS (Parallel Analysis of RNA Structure) is a high-throughput sequencing-based method used to study RNA structure and folding
FragSeq FragSeq (Fragmentation Sequencing) is a high-throughput sequencing-based method used to study RNA structure and folding
APEX-RIP APEX-RIP (Ascorbate Peroxidase Proximity-Dependent Biotinylation with RNA Interaction Profiling) is a method used to identify RNA-protein interactions on a transcriptome-wide scale.
Biochemical Fractionation + RNA-Seq A method combining biochemical fractionation of cells and high-throughput RNA sequencing that enables rapid and efficient systematic mapping of RNA cytotopic distributions in cells.