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 Experiment Video

Updated: Jun 14, 2026

Assessing Signaling Properties of Ectodermal Epithelia During Craniofacial Development
09:25

Assessing Signaling Properties of Ectodermal Epithelia During Craniofacial Development

Published on: March 24, 2011

Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks.

Felix Naef1, Joerg Huelsken

  • 1Swiss Institute for Experimental Cancer Research (ISREC), NCCR Molecular Oncology Chemin des Boveresses 155, 1066 Epalinges, Switzerland.

Nucleic Acids Research
|July 21, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates.

eLife·2026
Same author

Intestinal stem and progenitor cells exhibit distinct adaptive responses to inflammatory stress in IBD.

Stem cell research & therapy·2025
Same author

Conditional deep learning model reveals translation elongation determinants during amino acid deprivation.

Communications biology·2025
Same author

Molecular Systems Biology at 20: reflecting on the past, envisioning the future.

Molecular systems biology·2025
Same author

Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation.

Genome biology·2025
Same author

Daily liver rhythms: Coupling morphological and molecular oscillations.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

This study introduces a novel method for measuring cell-specific gene expression in mixed human-mouse samples without cell separation. This technique enables accurate transcriptional profiling in chimeric models, advancing research in tissue homeostasis and disease.

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Cell-type-specific transcriptional profiling is crucial for understanding complex biological processes like inflammation and tissue homeostasis.
  • Analyzing mixed cell populations is challenging due to the difficulty of separating distinct cell types within a tissue.
  • Existing methods often require physical cell separation, which can be labor-intensive and may alter cellular characteristics.

Purpose of the Study:

  • To develop a novel computational method for cell-type-specific gene expression measurement without prior cell separation.
  • To enable accurate transcriptional profiling in inter-species chimeric models, specifically using human-mouse systems.
  • To facilitate the study of cross-talk between different cell types in various biological contexts.

Main Methods:

More Related Videos

TChIP-Seq: Cell-Type-Specific Epigenome Profiling
07:28

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

Published on: January 23, 2019

Isolate Cell-Type-Specific RNAs from Snap-Frozen Heterogeneous Tissue Samples without Cell Sorting
08:30

Isolate Cell-Type-Specific RNAs from Snap-Frozen Heterogeneous Tissue Samples without Cell Sorting

Published on: December 8, 2021

Related Experiment Videos

Last Updated: Jun 14, 2026

Assessing Signaling Properties of Ectodermal Epithelia During Craniofacial Development
09:25

Assessing Signaling Properties of Ectodermal Epithelia During Craniofacial Development

Published on: March 24, 2011

TChIP-Seq: Cell-Type-Specific Epigenome Profiling
07:28

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

Published on: January 23, 2019

Isolate Cell-Type-Specific RNAs from Snap-Frozen Heterogeneous Tissue Samples without Cell Sorting
08:30

Isolate Cell-Type-Specific RNAs from Snap-Frozen Heterogeneous Tissue Samples without Cell Sorting

Published on: December 8, 2021

  • Exploited divergent human and mouse transcriptomes using high-density oligonucleotide arrays.
  • Developed a masking procedure based on transcriptome databases and fuzzy mapping of oligonucleotide probes.
  • Validated the approach in a human-mouse chimeric experiment analyzing mixed RNA samples.

Main Results:

  • Successfully measured species-specific transcriptional profiles in chimeric RNA samples without physical cell separation.
  • Demonstrated the effectiveness of transcriptome databases with accurate 3' mRNA termination for computational probe mask prediction.
  • Identified unique stretches in human and mouse 3'-untranslated regions crucial for controlling cross-hybridization.

Conclusions:

  • The developed method provides an efficient way to perform cell-type-specific expression measurements in mixed populations.
  • Accurate transcriptome databases are vital for computational prediction of probe masks in cross-species analyses.
  • This approach has broad applications in studying xenograft models, tumor-host interactions, morphogenesis, and immune responses.