Transcriptome Profiling
Transcriptome Profiling - Related Videos
10:22
Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
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2025
This article presents a protocol to perform comprehensive spatial transcriptomic profiling of host, viral, fungal, and microbiome RNA from formalin-fixed paraffin-embedded tissue sections using Stereo-seq, which enables high-resolution mapping of diverse transcriptomes while preserving tissue architecture.
09:45
Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level
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Cited by 6 •
2022
The protocol describes the isolation, culture, and profiling of endothelial cells from human mesenteric artery. Additionally, a method is provided to prepare human artery for spatial transcriptomics. Proteomics, transcriptomics, and functional assays can be performed on isolated cells. This protocol can be repurposed for any medium- or large-size artery.
02:52
Inducing the Prophage Lytic Replication for Transcriptomic Analysis
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2026
Source: Krishnamurthi, R., et al. Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics. J. Vis. Exp. (2024)This video demonstrates the induction of lytic replication in a prophage integrated into the bacterial genome and the capture of gene expression changes through timed sampling for transcriptomic analysis.
10:16
Mining Spatial Transcriptomics Datasets using DeepSpaceDB
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2025
This article introduces a protocol for using DeepSpaceDB, a dynamic, interactive database for spatial transcriptomics, offering analysis workflows and examples to explore tissue organization and disease-related gene expression.
07:18
Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
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2020
A method for transcriptome profiling of cereals is presented. The microarray-based gene expression profiling starts with the isolation of high-quality total RNA from cereal grains and continues with the generation of cDNA. After cRNA labelling and microarray hybridization, recommendations are given for signal detection and quality control.
FAQs
RNA levels reflect gene activity at the time and place sampled, so they can shift as cells encounter environmental signals, progress through development, or become diseased. This temporal and tissue-specific sensitivity helps distinguish cellular states and reveals coordinated responses that may not be apparent from a static description of the organism.
Sequencing-based and hybridization-based methods provide alternative routes for quantifying transcripts after sample preparation. They differ in how transcript measurements are generated, yet both can support comparisons among biological samples. Those comparisons help identify expression patterns associated with healthy or diseased tissue, developmental conditions, or environmental signals, depending on the study design.
Computational analysis compares transcript measurements to identify expression patterns and differentially expressed genes, meaning genes whose measured activity differs between conditions. These results can reveal coordinated changes in gene expression and suggest regulatory pathways for further investigation. The resulting patterns help researchers generate testable hypotheses about cellular function, disease mechanisms, or therapeutic targets.
Converting messenger RNA into complementary DNA creates the form used in common profiling workflows before transcript quantification. This step links the original RNA population to downstream sequencing or hybridization-based measurement, allowing transcript abundance to be assessed systematically across samples and compared for expression patterns and responses.
A typical workflow begins with RNA extraction from a cell, tissue, or organism. Messenger RNA is then converted into complementary DNA, followed by transcript quantification using high-throughput sequencing or a hybridization-based method. Computational analysis subsequently examines the measurements for expression patterns and differential expression, connecting laboratory processing with biological interpretation.
Researchers use transcriptome profiling when they need to compare gene activity across cellular or tissue conditions. Applications include characterizing cell types, contrasting healthy and diseased tissues, and examining responses to environmental or developmental signals. These comparisons can expose condition-associated expression changes and help focus later experiments on relevant biological pathways.
The analysis can reveal coordinated changes across groups of genes rather than isolated transcript differences. Such patterns may identify regulatory pathways associated with cellular function, disease mechanisms, or responses to external and developmental signals. Because the findings generate testable hypotheses, they can guide subsequent biological studies and the investigation of possible therapeutic targets.