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Profiling tissue-resident T cell repertoires by RNA sequencing
Deep sequencing of recombined T cell receptor (TCR) genes and transcripts has provided a view of T cell repertoire diversity at an unprecedented resolution. Beyond profiling peripheral blood, analysis of tissue-resident T cells provides further insight into immune-related diseases. We describe the e...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666197/ https://www.ncbi.nlm.nih.gov/pubmed/26620832 http://dx.doi.org/10.1186/s13073-015-0248-x |
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author | Brown, Scott D. Raeburn, Lisa A. Holt, Robert A. |
author_facet | Brown, Scott D. Raeburn, Lisa A. Holt, Robert A. |
author_sort | Brown, Scott D. |
collection | PubMed |
description | Deep sequencing of recombined T cell receptor (TCR) genes and transcripts has provided a view of T cell repertoire diversity at an unprecedented resolution. Beyond profiling peripheral blood, analysis of tissue-resident T cells provides further insight into immune-related diseases. We describe the extraction of TCR sequence information directly from RNA-sequencing data from 6738 tumor and 604 control tissues, with a typical yield of 1 TCR per 10 million reads. This method circumvents the need for PCR amplification of the TCR template and provides TCR information in the context of global gene expression, allowing integrated analysis of extensive RNA-sequencing data resources. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-015-0248-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4666197 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-46661972015-12-02 Profiling tissue-resident T cell repertoires by RNA sequencing Brown, Scott D. Raeburn, Lisa A. Holt, Robert A. Genome Med Method Deep sequencing of recombined T cell receptor (TCR) genes and transcripts has provided a view of T cell repertoire diversity at an unprecedented resolution. Beyond profiling peripheral blood, analysis of tissue-resident T cells provides further insight into immune-related diseases. We describe the extraction of TCR sequence information directly from RNA-sequencing data from 6738 tumor and 604 control tissues, with a typical yield of 1 TCR per 10 million reads. This method circumvents the need for PCR amplification of the TCR template and provides TCR information in the context of global gene expression, allowing integrated analysis of extensive RNA-sequencing data resources. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-015-0248-x) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-30 /pmc/articles/PMC4666197/ /pubmed/26620832 http://dx.doi.org/10.1186/s13073-015-0248-x Text en © Brown et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Method Brown, Scott D. Raeburn, Lisa A. Holt, Robert A. Profiling tissue-resident T cell repertoires by RNA sequencing |
title | Profiling tissue-resident T cell repertoires by RNA sequencing |
title_full | Profiling tissue-resident T cell repertoires by RNA sequencing |
title_fullStr | Profiling tissue-resident T cell repertoires by RNA sequencing |
title_full_unstemmed | Profiling tissue-resident T cell repertoires by RNA sequencing |
title_short | Profiling tissue-resident T cell repertoires by RNA sequencing |
title_sort | profiling tissue-resident t cell repertoires by rna sequencing |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666197/ https://www.ncbi.nlm.nih.gov/pubmed/26620832 http://dx.doi.org/10.1186/s13073-015-0248-x |
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