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Related Concept Videos

RNA-seq03:21

RNA-seq

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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
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Alternative RNA Splicing02:18

Alternative RNA Splicing

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Updated: Jan 29, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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CeL-ID: cell line identification using RNA-seq data.

Tabrez A Mohammad1, Yun S Tsai1, Safwa Ameer1

  • 1Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.

BMC Genomics
|February 5, 2019
PubMed
Summary
This summary is machine-generated.

A new RNA-sequencing based method, CeL-ID, accurately authenticates cell lines by analyzing unique genetic variants. This cost-effective approach identifies cell line identity and estimates cross-contamination, improving biomedical research quality.

Keywords:
CeL-IDCell line authenticationCell line identificationMutationRNA-Seq variant profilesSNP/Indel

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Area of Science:

  • Biotechnology
  • Genomics
  • Cancer Research

Background:

  • Cell lines are crucial for biological and cancer research.
  • Cell line contamination is a significant issue in biomedical science.
  • Current authentication methods are often inaccessible, complex, and time-consuming.

Purpose of the Study:

  • To develop a novel, cost-effective RNA-sequencing (RNA-seq) based approach for cell line authentication and quality control.
  • To establish a reliable method for identifying cell line identity and detecting cross-contamination.

Main Methods:

  • Developed CeL-ID, an RNA-seq based method for cell line authentication.
  • Generated cell line-specific variant profiles from RNA-seq data of 934 CCLE cell lines.
  • Calculated pair-wise correlations of variant profiles using variant frequencies and coverage depth.
  • Employed a linear mixture model to estimate cross-contamination.

Main Results:

  • RNA-seq based variant profiles are distinct for each cell line.
  • Identical, synonymous, and derivative cell lines exhibit high variant profile correlation (ρ > 0.9).
  • CeL-ID accurately identifies cell lines and can estimate cross-contamination.

Conclusions:

  • RNA-sequencing based variant profiles serve as a discriminatory feature for cell line authentication.
  • CeL-ID offers a valuable tool for improving cell line authentication in biomedical research.
  • The distinctness of variant profiles enables reliable identification and quality control of cell lines.