《差异基因表达谱分析技术》相关实验技术-Long Noncoding RNAs 2nd.pptxVIP

Long Noncoding RNAs: Genomics, Functions, Methodologies, Modes of ActionsWei Guifeng, mailto:guifengwei@guifengwei@Institute of Biophysics, Chinese Academy of Sciences2Pipeline for RNA-seq analysisReads(FASTQ)FASTQCMappingTophat2, STAR, SpliceMap, ……Transcriptome AssemblyCufflinks, Scripture, Trinity, ……Cufflinks, CuffnormCuffcompareNovel transcriptsQuantificationCuffdiff, edgeR, DEG, DESeq, ……Differentially Expressed GenesData File Format BED, GeneBed, GenePred, GTF/GFF Wig, Bigwig, BedGraph Fasta/FASTQ, SAM/BAM, VCF/BCF/FAQ/FAQformat.html/FAQ/FAQformat.htmlChIRP(CHART, RAP)-seq Chromatin isolation by RNA purification capture hybridization of RNA targets RNA antisense purificationCi Chu et al. Mol Cell 2011ChIRP(CHART, RAP)-seqMolecular CellPNASScienceChIRP(CHART, RAP)-seq HOTAIR (Ci Chu et al. Mol Cell 2011) Xist (Jesse M. Engreitz et al. Science 2013, Matthew D. Simon et al. Nature 2013) Paupar (Keith W Vance et al. EMBO J 2014) Dali (Vladislava Chalei et al. eLife 2014) NEAT1 and MALAT1 (Jason A. West et al. Mol Cell 2014) PCGEM1 (Liuqing Yang et al. Nature 2013)ChIRP(CHART, RAP)-seqprotocol/video/3912/chromatin-isolation-by-rna-purification-chirp/video/3912/chromatin-isolation-by-rna-purification-chirpLong noncoding RNAs may function as organizing factors that shape the cell nucleus.Rinn and Guttman. Science 2014Genomic Landscape of NEAT1 and MALAT1 locilncRNACO1CO2CHART enriches the lncRNAs NEAT1 and MALAT1.NEAT1 and MALAT1 localize to Actively Transcribed Genomic LociNEAT1 and MALAT1 localize to Actively Transcribed Genomic LociNEAT1 and MALAT1 localize to Genomic Sites in trans.ChIRP(CHART, RAP)-seqWhich lncRNAs are suitable for ChIRP-seq analysis ? high abundance act in trans localization in nucleus, special with chromatinThank you