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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...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2005
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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. |
format | Text |
id | pubmed-1178007 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT naeffelix celltypespecifictranscriptomicsinchimericmodelsusingtranscriptomebasedmasks AT huelskenjoerg celltypespecifictranscriptomicsinchimericmodelsusingtranscriptomebasedmasks |