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

Regulated mRNA Transport02:22

Regulated mRNA Transport

6.3K
In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
6.3K
Ribosome Profiling02:24

Ribosome Profiling

3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

23.3K
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
23.3K
DNA Microarrays02:34

DNA Microarrays

17.3K
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...
17.3K
Reporter Genes02:11

Reporter Genes

11.3K
Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
11.3K
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

4.6K
4.6K

You might also read

Related Articles

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

Sort by
Same author

Evolutionarily informed gene sets reveal conserved and lineage-modified transcriptional programs during vertebrate forebrain evolution.

bioRxiv : the preprint server for biology·2026
Same author

Deconvolving cell-type-specific gene expression profiles from bulk RNA-seq samples.

PLoS computational biology·2026
Same author

Programming T cells for Early Cancer Detection with Customized Protease-Activatable Receptors.

bioRxiv : the preprint server for biology·2026
Same author

Clustering Analysis of Multiple Omics Data Types Identifies Cancer Patients With Consistent Survival Outcomes.

Cancer informatics·2025
Same author

Recursive Clustering of Cellular Diversity in scRNA-Seq Data.

Journal of computational biology : a journal of computational molecular cell biology·2025
Same author

AND-gated protease-activated nanosensors for programmable detection of anti-tumour immunity.

Nature nanotechnology·2025
Same journal

CNV-ECOD: A copy number variation detection method based on ECOD algorithm using next-generation sequencing data.

Journal of bioinformatics and computational biology·2026
Same journal

ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation.

Journal of bioinformatics and computational biology·2026
Same journal

When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis.

Journal of bioinformatics and computational biology·2026
Same journal

Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for IsPETase structure prediction.

Journal of bioinformatics and computational biology·2026
Same journal

Trap spaces as labelled ideals of SCC posets: A structural-functional theory of reachability in asynchronous boolean networks.

Journal of bioinformatics and computational biology·2026
Same journal

Erratum - DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder.

Journal of bioinformatics and computational biology·2026
See all related articles

Related Experiment Video

Updated: Jun 20, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

4.9K

Gene representation bias in spatial transcriptomics.

Xinling Li1, Peng Qiu1

  • 1The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States.

Journal of Bioinformatics and Computational Biology
|July 22, 2024
PubMed
Summary
This summary is machine-generated.

Spatial transcriptomics (Visium) often under-detects certain genes compared to bulk RNA-seq. This under-detection is linked to a poly (T) motif, potentially hindering mRNA capture during library preparation.

Keywords:
Spatial transcriptomicsbulk RNA-seqsparsity

More Related Videos

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord
11:13

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

Published on: November 1, 2014

14.6K
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

9.5K

Related Experiment Videos

Last Updated: Jun 20, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

4.9K
RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord
11:13

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

Published on: November 1, 2014

14.6K
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

9.5K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Spatial transcriptomics, particularly Visium, generates sparse gene-spot count matrices, similar to single-cell RNA sequencing.
  • Understanding data sparsity and gene detection biases is crucial for accurate spatial gene expression analysis.

Purpose of the Study:

  • To identify genes frequently under-detected in Visium spatial transcriptomics compared to bulk RNA sequencing.
  • To investigate the underlying molecular mechanisms responsible for this under-detection bias.

Main Methods:

  • Comparative analysis of paired Visium and bulk RNA sequencing data from 28 human and 19 mouse samples.
  • Motif enrichment analysis of the 350 bp region upstream of the transcription start site for under-detected genes.

Main Results:

  • A distinct set of genes was consistently under-detected in Visium data across both human and mouse samples when compared to bulk RNA sequencing.
  • The poly (T) motif was significantly enriched in these under-detected genes in both species.

Conclusions:

  • Genes with enriched poly (T) motifs are prone to under-detection in Visium spatial transcriptomics.
  • The poly (T) motif may facilitate hairpin structure formation with mRNA poly (A) tails, impeding transcript capture during library preparation.