title: An atlas of mouse CD4(+) T cell transcriptomes.
abstract: BACKGROUND
  CD4(+) T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of several effector subtypes that exhibit distinct functions. The transcriptional mechanisms that underlie the specific functional identity of CD4(+) T cells are not fully understood.
  
  
  RESULTS
  To assist investigations into the transcriptional identity and regulatory processes of these cells we performed mRNA-sequencing on three murine T helper subtypes (Th1, Th2 and Th17) as well as on splenic Treg cells and induced Treg (iTreg) cells. Our integrated analysis of this dataset revealed the gene expression changes associated with these related but distinct cellular identities. Each cell subtype differentially expresses a wealth of 'subtype upregulated' genes, some of which are well known whilst others promise new insights into signalling processes and transcriptional regulation. We show that hundreds of genes are regulated purely by alternative splicing to extend our knowledge of the role of post-transcriptional regulation in cell differentiation.
  
  
  CONCLUSIONS
  This CD4(+) transcriptome atlas provides a valuable resource for the study of CD4(+) T cell populations. To facilitate its use by others, we have made the data available in an easily accessible online resource at www.th-express.org.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. mstubb@ebi.ac.uk.
authors.forename: Michael Jt
authors.initials: MJ
authors.lastname: Stubbington
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. bmahata@ebi.ac.uk.|Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. bmahata@ebi.ac.uk.
authors.forename: Bidesh
authors.initials: B
authors.lastname: Mahata
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. vale@ebi.ac.uk.
authors.forename: Valentine
authors.initials: V
authors.lastname: Svensson
authors.affiliation: MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK. andrew_deo@hotmail.com.
authors.forename: Andrew
authors.initials: A
authors.lastname: Deonarine
authors.affiliation: MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK. jesper.klinto@gmail.com.
authors.forename: Jesper K
authors.initials: JK
authors.lastname: Nissen
authors.affiliation: MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK. betz@ebi.ac.uk.
authors.forename: Alexander G
authors.initials: AG
authors.lastname: Betz
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. saraht@ebi.ac.uk.|Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. saraht@ebi.ac.uk.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Teichmann
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D002454:Cell Differentiation; D016000:Cluster Analysis; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D007107:Immune System; D051379:Mice; D008810:Mice, Inbred C57BL; D025341:Principal Component Analysis; D020033:Protein Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D006377:T-Lymphocytes, Helper-Inducer / Q000166:cytology*; D050378:T-Lymphocytes, Regulatory / Q000166:cytology*; D058504:Th17 Cells / Q000166:cytology*; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger