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Related Concept Videos

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...
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...

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Related Experiment Video

Updated: Jul 12, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
10:22

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

Analysis of isoform complexity in pan-transcriptome graphs with atroplex.

Richard A Schäfer, Yangyang Li, Joshua Fry

    Biorxiv : the Preprint Server for Biology
    |July 10, 2026
    PubMed
    Summary

    A new framework, atroplex, indexes complex RNA splicing data for efficient analysis. This tool enables researchers to compare transcript structures across many samples, improving the discovery of novel RNA isoforms.

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    A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
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    A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

    Published on: December 2, 2009

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    Last Updated: Jul 12, 2026

    Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
    10:22

    Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

    Published on: October 31, 2025

    A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
    13:00

    A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

    Published on: December 2, 2009

    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Alternative splicing allows a single gene to produce multiple RNA isoforms.
    • Long-read sequencing reveals extensive transcript diversity across biological samples.
    • Analyzing complex pan-transcriptomes requires efficient indexing for comparison.

    Purpose of the Study:

    • To develop a queryable index for complex pan-transcriptome data.
    • To enable structural comparison of RNA isoforms across different cohorts.
    • To facilitate the discovery of novel transcript isoforms.

    Main Methods:

    • Introduced atroplex, a framework combining spatial indexing and graph overlays.
    • Indexed pan-transcriptome annotations and transcript isoforms.
    • Developed methods for classifying query transcripts and tracking isoform presence.

    Main Results:

    • atroplex creates a unified, queryable structure for 21,005 samples.
    • The framework captures both exon coordinates and splice junction connectivity.
    • Enabled comprehensive mapping of isoform complexity and cross-cohort comparisons.

    Conclusions:

    • atroplex provides an efficient solution for analyzing large-scale transcriptomic data.
    • The tool enhances transcript discovery and structural isoform comparison.
    • This indexing approach is crucial for understanding splicing variations across conditions.