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

Regulatory networks involving different cell types control inflammation, morphogenesis and tissue homeostasis. Cell-type-specific transcriptional profiling offers a powerful tool for analyzing such cross-talk but is often hampered by mingling of cells within a tissue. Here, we present a novel method...

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Detalles Bibliográficos
Autores principales: Naef, Felix, Huelsken, Joerg
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1178007/
https://www.ncbi.nlm.nih.gov/pubmed/16030348
http://dx.doi.org/10.1093/nar/gni104
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author Naef, Felix
Huelsken, Joerg
author_facet Naef, Felix
Huelsken, Joerg
author_sort Naef, Felix
collection PubMed
description Regulatory networks involving different cell types control inflammation, morphogenesis and tissue homeostasis. Cell-type-specific transcriptional profiling offers a powerful tool for analyzing such cross-talk but is often hampered by mingling of cells within a tissue. Here, we present a novel method that performs cell-type-specific expression measurements without prior cell separation. This involves inter-species transplantation or chimeric co-culture models among which the human mouse system is frequently used. Here, we exploit the sufficiently divergent transcriptomes of human and mouse in conjunction with high-density oligonucleotide arrays. This required a masking procedure based on transcriptome databases and exhaustive fuzzy mapping of oligonucleotide probes onto these data. The approach was tested in a human–mouse experiment, demonstrating that we can efficiently measure species-specific transcriptional profiles in chimeric RNA samples without physically separating cells. Our results stress the importance of transcriptome databases with accurate 3′ mRNA termination for computational prediction of accurate probe masks. We find that most human and mouse 3′-untranslated region contain unique stretches to allow for an effective control of cross-hybridization between the two species. This approach can be applied to xenograft models studying tumor–host interactions, morphogenesis or immune responses.
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spelling pubmed-11780072005-07-21 Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks Naef, Felix Huelsken, Joerg Nucleic Acids Res Methods Online Regulatory networks involving different cell types control inflammation, morphogenesis and tissue homeostasis. Cell-type-specific transcriptional profiling offers a powerful tool for analyzing such cross-talk but is often hampered by mingling of cells within a tissue. Here, we present a novel method that performs cell-type-specific expression measurements without prior cell separation. This involves inter-species transplantation or chimeric co-culture models among which the human mouse system is frequently used. Here, we exploit the sufficiently divergent transcriptomes of human and mouse in conjunction with high-density oligonucleotide arrays. This required a masking procedure based on transcriptome databases and exhaustive fuzzy mapping of oligonucleotide probes onto these data. The approach was tested in a human–mouse experiment, demonstrating that we can efficiently measure species-specific transcriptional profiles in chimeric RNA samples without physically separating cells. Our results stress the importance of transcriptome databases with accurate 3′ mRNA termination for computational prediction of accurate probe masks. We find that most human and mouse 3′-untranslated region contain unique stretches to allow for an effective control of cross-hybridization between the two species. This approach can be applied to xenograft models studying tumor–host interactions, morphogenesis or immune responses. Oxford University Press 2005 2005-07-19 /pmc/articles/PMC1178007/ /pubmed/16030348 http://dx.doi.org/10.1093/nar/gni104 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Methods Online
Naef, Felix
Huelsken, Joerg
Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
title Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
title_full Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
title_fullStr Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
title_full_unstemmed Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
title_short Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
title_sort cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1178007/
https://www.ncbi.nlm.nih.gov/pubmed/16030348
http://dx.doi.org/10.1093/nar/gni104
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