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

3.0K
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...
3.0K

You might also read

Related Articles

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

Sort by
Same author

HERA: a web server for host element reference-based aligner.

Nucleic acids research·2026
Same author

Continental-wide prioritization of protected areas to address global and habitat-specific goals for avian biodiversity conservation.

Conservation biology : the journal of the Society for Conservation Biology·2026
Same author

RegRegSEA: a web server for regulatory region set enrichment analysis of epigenomic data.

Nucleic acids research·2026
Same author

Providing regular and frequent maps of losses and gains of farmland birds based on European monitoring data.

Conservation biology : the journal of the Society for Conservation Biology·2026
Same author

mRNA Sequencing of Limbal Epithelial Cells and mRNA/miRNA Profiling of Limbal Stromal Cells in <i>PAX6</i>-Related Congenital Aniridia.

Cells·2026
Same author

MCPmed: a call for Model Context Protocol-enabled bioinformatics web services for LLM-driven discovery.

Briefings in bioinformatics·2026

Related Experiment Video

Updated: Jun 29, 2025

mirMachine: A One-Stop Shop for Plant miRNA Annotation
06:16

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

2.5K

SingmiR: a single-cell miRNA alignment and analysis tool.

Annika Engel1, Shusruto Rishik1, Pascal Hirsch1

  • 1Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.

Nucleic Acids Research
|April 4, 2024
PubMed
Summary
This summary is machine-generated.

SingmiR offers a user-friendly web server for processing single-cell miRNA sequencing data. This tool accelerates the analysis of microRNA regulation in individual cells, aiding biological discoveries.

More Related Videos

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
08:49

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

7.6K
A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
00:09

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

Published on: August 21, 2019

7.3K

Related Experiment Videos

Last Updated: Jun 29, 2025

mirMachine: A One-Stop Shop for Plant miRNA Annotation
06:16

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

2.5K
Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
08:49

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

7.6K
A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
00:09

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

Published on: August 21, 2019

7.3K

Area of Science:

  • Genomics and Molecular Biology
  • Bioinformatics and Computational Biology

Background:

  • Single-cell RNA sequencing (RNA-seq) has advanced cell biology but leaves microRNA (miRNA) regulatory processes largely unexplored at the single-cell level.
  • Analyzing single-cell miRNA sequencing (miRNA-seq) data requires advanced computational skills, and a dedicated, user-friendly workflow is lacking.

Purpose of the Study:

  • To present SingmiR, a novel web server designed for the rapid preprocessing and quantification of human single-cell miRNA-seq data.
  • To provide biologists with an accessible computational tool to facilitate the analysis of miRNA expression and regulation in individual cells.

Main Methods:

  • Developed a web server implementing a comprehensive workflow for single-cell miRNA-seq data.
  • Included functionalities for read trimming, automated quality control, and feature normalization.
  • Integrated standard and advanced analytical modules like dimension reduction, heatmaps, and differential expression analysis.

Main Results:

  • SingmiR enables efficient preprocessing and quantification of human miRNAs from single-cell samples.
  • The server provides automated quality control reports and normalized count files.
  • Offers diverse analytical tools to expedite the prototyping of single-cell miRNA-seq protocols for small to medium datasets.

Conclusions:

  • SingmiR addresses the need for a specialized, user-friendly computational tool for single-cell miRNA-seq data analysis.
  • The platform aims to accelerate research into post-transcriptional gene regulation by miRNAs at the single-cell level.
  • SingmiR is freely accessible, promoting wider adoption and advancement in the field.