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Related Concept Videos

RNA-seq03:21

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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. 
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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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siRNA - Small Interfering RNAs02:30

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Related Experiment Video

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Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
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Identification and annotation of small RNA genes using ShortStack.

Saima Shahid1, Michael J Axtell1

  • 1Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Department of Biology, Penn State University, University Park, PA 16802, USA.

Methods (San Diego, Calif.)
|October 22, 2013
PubMed
Summary

This tutorial introduces ShortStack, a powerful tool for analyzing small RNA sequencing (small RNA-seq) data. It helps researchers annotate small RNA-producing genes by processing sequencing reads and identifying precursor RNAs.

Keywords:
BioinformaticsGenome annotationHigh-throughput sequencingSmall RNAmicroRNAsiRNA

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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Small RNA sequencing (small RNA-seq) is crucial for understanding eukaryotic regulatory small RNAs.
  • Regulatory small RNAs, including microRNAs (miRNAs), short interfering RNAs (siRNAs), and Piwi-associated RNAs (piRNAs), are derived from precursor RNAs.
  • Genome alignment of small RNA-seq data enables inference of precursor RNAs and annotation of small RNA-producing genes.

Purpose of the Study:

  • To provide a comprehensive tutorial for using the ShortStack program.
  • To introduce new users to ShortStack's capabilities for analyzing small RNA-seq data.
  • To guide users in annotating small RNA-producing genes and identify potential pitfalls.

Main Methods:

  • Utilizing ShortStack for comprehensive analysis of reference-aligned small RNA-seq data.
  • Step-by-step guidance on ShortStack software usage.
  • Demonstrating the inference of precursor RNAs from aligned small RNA reads.

Main Results:

  • Detailed and useful annotations of causal small RNA-producing genes.
  • Facilitation of the identification and characterization of miRNA, siRNA, and piRNA loci.
  • Practical insights into common challenges and solutions when using ShortStack.

Conclusions:

  • ShortStack is an effective tool for annotating small RNA-producing genes from small RNA-seq data.
  • This tutorial serves as a valuable resource for researchers new to small RNA-seq analysis.
  • Proper utilization of ShortStack enhances the understanding of regulatory small RNA biogenesis.