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RNA Detection

Overview of attention for book
Cover of 'RNA Detection'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 The Secret Life of RNA: Lessons from Emerging Methodologies
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    Chapter 2 Quantification of 2′-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
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    Chapter 3 Identifying the m6A Methylome by Affinity Purification and Sequencing
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    Chapter 4 PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution
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    Chapter 5 Axon-TRAP-RiboTag: Affinity Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo
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    Chapter 6 LCM-Seq: A Method for Spatial Transcriptomic Profiling Using Laser Capture Microdissection Coupled with PolyA-Based RNA Sequencing
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    Chapter 7 Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas
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    Chapter 8 Single mRNA Molecule Detection in Drosophila
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    Chapter 9 Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos
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    Chapter 10 Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction
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    Chapter 11 Detection of mRNA and Associated Molecules by ISH-IEM on Frozen Sections
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    Chapter 12 Hybridization Chain Reaction for Direct mRNA Detection Without Nucleic Acid Purification
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    Chapter 13 In Situ Detection of MicroRNA Expression with RNAscope Probes
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    Chapter 14 Padlock Probes to Detect Single Nucleotide Polymorphisms
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    Chapter 15 Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons
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    Chapter 16 Optimizing Molecular Beacons for Intracellular Analysis of RNA
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    Chapter 17 Live Imaging of Nuclear RNPs in Mammalian Complex Tissue with ECHO-liveFISH
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    Chapter 18 In Vivo Visualization and Function Probing of Transport mRNPs Using Injected FIT Probes
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    Chapter 19 Visualizing RNA in Live Bacterial Cells Using Fluorophore- and Quencher-Binding Aptamers
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    Chapter 20 Method for Imaging Live-Cell RNA Using an RNA Aptamer and a Fluorescent Probe
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    Chapter 21 RNA Live Imaging in the Model Microorganism Ustilago maydis
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    Chapter 22 Real-Time Fluorescence Imaging of Single-Molecule Endogenous Noncoding RNA in Living Cells
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    Chapter 23 Live Imaging of mRNA Synthesis in Drosophila
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    Chapter 24 Imaging Newly Transcribed RNA in Cells by Using a Clickable Azide-Modified UTP Analog
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    Chapter 25 Detection of the First Round of Translation: The TRICK Assay
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    Chapter 26 Imaging Translation Dynamics of Single mRNA Molecules in Live Cells
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    Chapter 27 Systematic Detection of Poly(A)+ RNA-Interacting Proteins and Their Differential Binding
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    Chapter 28 Isolation and Characterization of Endogenous RNPs from Brain Tissues
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    Chapter 29 Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein–RNA Interactions
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    Chapter 30 RNA Tagging: Preparation of High-Throughput Sequencing Libraries
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    Chapter 31 RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells
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    Chapter 32 Erratum to: Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction
Attention for Chapter 14: Padlock Probes to Detect Single Nucleotide Polymorphisms
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Chapter title
Padlock Probes to Detect Single Nucleotide Polymorphisms
Chapter number 14
Book title
RNA Detection
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7213-5_14
Pubmed ID
Book ISBNs
978-1-4939-7212-8, 978-1-4939-7213-5
Authors

Tomasz Krzywkowski, Mats Nilsson, Krzywkowski, Tomasz, Nilsson, Mats

Abstract

Rapid development of high-throughput DNA analyzation methods has enabled global characterization of genetic landscapes and aberrations in study subjects in a time and cost effective fashion. In most methods, however, spatial tissue context is lost since sample preparation requires isolation of nucleic acids out of their native environment. We hereby present the most recent protocol for multiplexed, in situ detection of mRNAs and single nucleotide polymorphisms using padlock probes and rolling circle amplification. We take advantage of a single nucleotide variant within conserved ACTB mRNA to successfully differentiate human and mice cocultured cells and apply presented protocol to genotype PCDH X and Y homologs in human brain. We provide a method for automated characterization and quantitation of target mRNA in single cells or chosen tissue area. mRNA of interest, harboring a polymorphism, is first reverse-transcribed to cDNA. Allele specific padlock probes are hybridized to the cDNA target and enzymatically circularized maintaining a physical link with the parent mRNA molecule. Lastly, circularized probes are replicated in situ, using rolling circle amplification mechanism to facilitate detection.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 18 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 4 22%
Student > Ph. D. Student 3 17%
Student > Bachelor 3 17%
Student > Master 2 11%
Unknown 6 33%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 39%
Agricultural and Biological Sciences 2 11%
Pharmacology, Toxicology and Pharmaceutical Science 1 6%
Physics and Astronomy 1 6%
Medicine and Dentistry 1 6%
Other 0 0%
Unknown 6 33%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 10 December 2020.
All research outputs
#7,294,779
of 23,008,860 outputs
Outputs from Methods in molecular biology
#2,216
of 13,157 outputs
Outputs of similar age
#147,995
of 442,295 outputs
Outputs of similar age from Methods in molecular biology
#214
of 1,498 outputs
Altmetric has tracked 23,008,860 research outputs across all sources so far. This one has received more attention than most of these and is in the 67th percentile.
So far Altmetric has tracked 13,157 research outputs from this source. They receive a mean Attention Score of 3.4. This one has done well, scoring higher than 82% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 442,295 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 65% of its contemporaries.
We're also able to compare this research output to 1,498 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 84% of its contemporaries.