Long Noncoding RNAs 2nd(1).pptx

Long Noncoding RNAs:Genomics,Functions,Methodologies,Modes of Actions,Wei Guifeng,Institute of Biophysics,Chinese Academy of Sciences,2,Reads(FASTQ),FASTQC,Mapping,Tophat2,STAR,SpliceMap,Transcriptome Assembly,Cufflinks,Scripture,Trinity,Novel transcripts,Quantification,Cuffcompare,Cufflinks,Cuffnorm,Differentially Expressed Genes,Cuffdiff,edgeR,DEG,DESeq,Pipeline for RNA-seq analysis,BED,GeneBed,GenePred,GTF/GFF Wig,Bigwig,BedGraph Fasta/FASTQ,SAM/BAM,VCF/BCF,Data File Format,http:/genome.ucsc.edu/FAQ/FAQformat.html,Ci Chu et al.Mol Cell 2011,ChIRP(CHART,RAP)-seq,Chromatin isolation by RNA purification capture hybridization of RNA targets RNA antisense purification,PNAS,Science,Molecular Cell,ChIRP(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)-seq,ChIRP(CHART,RAP)-seq,protocol,http:/,Long noncoding RNAs may function as organizing factors that shape the cell nucleus.,Rinn and Guttman.Science 2014,Genomic Landscape of NEAT1 and MALAT1 loci,lncRNA,CO1,CO2,CHART enriches the lncRNAs NEAT1 and MALAT1.,NEAT1 and MALAT1 localize to Actively Transcribed Genomic Loci,NEAT1 and MALAT1 localize to Actively Transcribed Genomic Loci,NEAT1 and MALAT1 localize to Genomic Sites in trans.,high abundance act in trans localization in nucleus,special with chromatin,ChIRP(CHART,RAP)-seq,Which lncRNAs are suitable for ChIRP-seq analysis?,Thank you,