dc.contributor.author | Afik, Shaked | en_US |
dc.contributor.author | Yates, Kathleen B. | en_US |
dc.contributor.author | Bi, Kevin | en_US |
dc.contributor.author | Darko, Samuel | en_US |
dc.contributor.author | Godec, Jernej | en_US |
dc.contributor.author | Gerdemann, Ulrike | en_US |
dc.contributor.author | Swadling, Leo | en_US |
dc.contributor.author | Douek, Daniel C. | en_US |
dc.contributor.author | Klenerman, Paul | en_US |
dc.contributor.author | Barnes, Eleanor J. | en_US |
dc.contributor.author | Sharpe, Arlene H. | en_US |
dc.contributor.author | Haining, W. Nicholas | en_US |
dc.contributor.author | Yosef, Nir | en_US |
dc.date.accessioned | 2018-02-26T20:42:34Z | |
dc.date.issued | 2017 | en_US |
dc.identifier.citation | Afik, S., K. B. Yates, K. Bi, S. Darko, J. Godec, U. Gerdemann, L. Swadling, et al. 2017. “Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state.” Nucleic Acids Research 45 (16): e148. doi:10.1093/nar/gkx615. http://dx.doi.org/10.1093/nar/gkx615. | en |
dc.identifier.issn | | en |
dc.identifier.uri | http://nrs.harvard.edu/urn-3:HUL.InstRepos:34868947 | |
dc.description.abstract | Abstract The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present TRAPeS, a publicly available tool that can efficiently extract TCR sequence information from short-read scRNA-seq libraries. We apply it to investigate heterogeneity in the CD8+ T cell response in humans and mice, and show that it is accurate and more sensitive than existing approaches. Coupling TRAPeS with transcriptome analysis of CD8+ T cells specific for a single epitope from Yellow Fever Virus (YFV), we show that the recently described ‘naive-like’ memory population have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype cells. This suggests that TCR usage is associated with the differentiation state of the CD8+ T cell response to YFV. | en |
dc.language.iso | en_US | en |
dc.publisher | Oxford University Press | en |
dc.relation.isversionof | doi:10.1093/nar/gkx615 | en |
dc.relation.hasversion | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766189/pdf/ | en |
dash.license | LAA | en_US |
dc.title | Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state | en |
dc.type | Journal Article | en_US |
dc.description.version | Version of Record | en |
dc.relation.journal | Nucleic Acids Research | en |
dash.depositing.author | Gerdemann, Ulrike | en_US |
dc.date.available | 2018-02-26T20:42:34Z | |
dc.identifier.doi | 10.1093/nar/gkx615 | * |
dash.authorsordered | false | |
dash.contributor.affiliated | Sharpe, Arlene | |
dash.contributor.affiliated | Gerdemann, Ulrike | |