Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Proof of Concept: Extended Reality-Assisted Resternotomy Planning for Complex Cardiac Surgery.

Brazilian journal of cardiovascular surgery·2026
Same author

Impact of Neck Dissection on Infrahyoid and Suprahyoid Muscle Dimensions in Head and Neck Cancer.

European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery·2026
Same author

A microRNA generated via lysosomal processing of ribosomal RNA suppresses proinflammatory responses.

Life science alliance·2026
Same author

3D Virtual reality assessment of right ventricle-pulmonary artery conduit dilation and coronary compression risk: a retrospective bi-center feasibility study.

Frontiers in cardiovascular medicine·2026
Same author

Pre-procedural three-dimensional computed tomography vs. angiographic assessment for patent ductus arteriosus stenting: a comparative analysis.

Frontiers in cardiovascular medicine·2026
Same author

Mapping the transcriptional landscape of algal resistance to viral infection reveals a core expression program.

The New phytologist·2025
Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026
Same journal

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026
Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026
Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026
Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026
Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026
See all related articles

Related Experiment Video

Updated: May 13, 2026

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method
09:06

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

Published on: October 7, 2025

Differences in microRNA detection levels are technology and sequence dependent.

Dena Leshkowitz1, Shirley Horn-Saban, Yisrael Parmet

  • 11Biological Services Department, Weizmann Institute of Science, Rehovot, Israel. dena.leshkowitz@weizmann.ac.il

RNA (New York, N.Y.)
|February 23, 2013
PubMed
Summary
This summary is machine-generated.

Comparing high-throughput platforms for small RNA detection revealed significant variations. Platform choice impacts microRNA (miRNA) detection accuracy, especially for modified or similar sequences, necessitating careful consideration of detection biases.

More Related Videos

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs
10:28

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs

Published on: April 14, 2015

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
09:29

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

Related Experiment Videos

Last Updated: May 13, 2026

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method
09:06

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

Published on: October 7, 2025

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs
10:28

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs

Published on: April 14, 2015

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
09:29

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Accurate identification and quantification of small RNAs, particularly microRNAs (miRNAs), are crucial but challenging due to their short length, sequence similarities, isoforms, and modifications.
  • Existing high-throughput platforms for miRNA analysis include microarrays (Agilent, Affymetrix) and next-generation sequencing (Illumina), each with potential biases.

Purpose of the Study:

  • To systematically compare the detection performance of Agilent and Affymetrix microarrays and Illumina next-generation sequencing for small RNA quantification.
  • To investigate how miRNA modifications (e.g., O-methyl 3') and sequence attributes influence detection accuracy across different platforms.
  • To identify and understand platform-dependent biases in miRNA expression detection.

Main Methods:

  • Systematic comparison of three commercial high-throughput platforms: Agilent microarrays, Affymetrix microarrays, and Illumina next-generation sequencing.
  • Utilized synthetic transcripts (mature, precursor, O-methyl-modified miRNAs) spiked into human RNA to assess detection performance under controlled conditions.
  • Assessed endogenous human miRNA expression levels across the platforms and analyzed attributes like base composition, sequence structure, and isoform characteristics.

Main Results:

  • Detection performance varied significantly across platforms, influenced by miRNA modifications and sequence characteristics.
  • A reduced capacity for detecting O-methyl-modified miRNAs and large intensity variations were observed across all tested platforms.
  • Endogenous miRNA expression levels were inconsistent between platforms, highlighting significant detection biases.

Conclusions:

  • Platform choice critically affects miRNA detection accuracy and quantification, particularly for modified or structurally similar miRNAs.
  • Understanding miRNA attributes (sequence, modifications, isoforms) is essential for interpreting and adjusting platform-specific detection biases.
  • This study provides a foundation for selecting appropriate platforms and developing strategies to mitigate detection biases in small RNA research.