title: Next-Generation Sequencing Analysis of Long Noncoding RNAs in CD4+ T Cell Differentiation.
abstract: Next-generation sequencing approaches, in particular RNA-seq, provide a genome-wide expression profiling allowing the identification of novel and rare transcripts such as long noncoding RNAs (lncRNA). Many RNA-seq studies have now been performed aimed at the characterization of lncRNAs and their possible involvement in cell development and differentiation in different organisms, cell types, and tissues. The adaptive immune system is an extraordinary context for the study of the role of lncRNAs in differentiation. Indeed lncRNAs seem to be key drivers in governing flexibility and plasticity of both CD8+and CD4+T cell, together with lineage-specific transcription factors and cytokines, acting as fine-tuners of fate choices in T cell differentiation.We describe here a pipeline for the identification of lncRNAs starting from RNA-Seq raw data.
authors: Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
authors: Valeria
authors: V
authors: Ranzani
authors: Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
authors: Alberto
authors: A
authors: Arrigoni
authors: Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
authors: Grazisa
authors: G
authors: Rossetti
authors: Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
authors: Ilaria
authors: I
authors: Panzeri
authors: Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.|Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via Festa del Perdono 7, Milan, 20122, Italy.
authors: Sergio
authors: S
authors: Abrignani
authors: Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy. bonnal@ingm.org.
authors: Raoul J P
authors: RJ
authors: Bonnal
authors: Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy. pagani@ingm.org.|Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Festa del Perdono 7, Milan, 20122, Italy. pagani@ingm.org.
authors: Massimiliano
authors: M
authors: Pagani
mesh_terms: D015496:CD4-Positive T-Lymphocytes / Q000276:immunology; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology; D002454:Cell Differentiation / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D062085:RNA, Long Noncoding / Q000235:genetics / Q000276:immunology*
chemical_list: D062085:RNA, Long Noncoding
keywords: Bioinformatics; CD4+ T cells; Immune system; NGS; RNA-seq; lncRNAs