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Keywords {🔍}

lncrnas, cells, cell, expression, pubmed, rnaseq, single, article, additional, file, genes, mrnas, singlecell, lncrna, google, scholar, fig, expressed, transcripts, neocortex, bulk, human, gene, polya, cas, figure, rna, tissues, total, brain, typespecific, performed, central, tissue, levels, ercc, detected, counts, reference, radial, samples, transcriptome, mrna, analysis, noncoding, types, type, median, loc, specific,

Topics {✒️}

{\theta}_{ij}= log\frac{p_{ij}\left library-type fr-firststrand --microexon-search single-cell rna-seq experiments strand-specific rna-seq alignments single-cell rna-seq libraries single-cell rna-seq analysis quantitative single-cell rna-seq genome-scale crispr-mediated control single-cell rna-seq reads single-cell rna-seq statistics performed strand-specific rna-seq single-cell rna-seq expression single-cell rna-seq sample paired-end 100 bp protocol dcas9-krab-bfp lentivirus tissue rna-seq experiments article download pdf dcas9-krab u87 cells coding-potential assessment tool heat-induced antigen retrieval ucsf-ctsi ul1 tr000004 strand-specific rna-seq dig-rna labeling mix interneuron-specific lncrna dlx6-as1 size factor-normalized counts puromycin-resistant lentiviral vectors single-cell rna-seq bulk tissue rna-seq = {\beta}_0+{\beta}_1{ prenatal human brain linear regression model total rna-seq libraries single-cell transcriptomics applied gene-level fragment counts bulk rna-seq data total rna-seq transcriptomes cell type-specific expression total rna-seq data polya selection rna-seq identified cell type-specific fluidigm c1 platform neuronal-glial fate specification polya rna-seq data conduct cell-type identification }_2+\dots +{\beta}_n{ polya selected rna-seq yield single-cell suspensions single-cell microfluidic capture regulates cell proliferation single-cell cdna libraries

Schema {🗺️}

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         headline:Single-cell analysis of long non-coding RNAs in the developing human neocortex
         description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and disease. LncRNAs exhibit cell type- and tissue-specific expression, but little is known about the expression and function of lncRNAs in the developing human brain. Furthermore, it has been unclear whether lncRNAs are highly expressed in subsets of cells within tissues, despite appearing lowly expressed in bulk populations. We use strand-specific RNA-seq to deeply profile lncRNAs from polyadenylated and total RNA obtained from human neocortex at different stages of development, and we apply this reference to analyze the transcriptomes of single cells. While lncRNAs are generally detected at low levels in bulk tissues, single-cell transcriptomics of hundreds of neocortex cells reveal that many lncRNAs are abundantly expressed in individual cells and are cell type-specific. Notably, LOC646329 is a lncRNA enriched in single radial glia cells but is detected at low abundance in tissues. CRISPRi knockdown of LOC646329 indicates that this lncRNA regulates cell proliferation. The discrete and abundant expression of lncRNAs among individual cells has important implications for both their biological function and utility for distinguishing neural cell types.
         datePublished:2016-04-14T00:00:00Z
         dateModified:2016-04-14T00:00:00Z
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         pageEnd:17
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            lncRNA
            Single-cell RNA-seq
            Developing brain
            CRISPRi
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:Single-cell analysis of long non-coding RNAs in the developing human neocortex
      description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and disease. LncRNAs exhibit cell type- and tissue-specific expression, but little is known about the expression and function of lncRNAs in the developing human brain. Furthermore, it has been unclear whether lncRNAs are highly expressed in subsets of cells within tissues, despite appearing lowly expressed in bulk populations. We use strand-specific RNA-seq to deeply profile lncRNAs from polyadenylated and total RNA obtained from human neocortex at different stages of development, and we apply this reference to analyze the transcriptomes of single cells. While lncRNAs are generally detected at low levels in bulk tissues, single-cell transcriptomics of hundreds of neocortex cells reveal that many lncRNAs are abundantly expressed in individual cells and are cell type-specific. Notably, LOC646329 is a lncRNA enriched in single radial glia cells but is detected at low abundance in tissues. CRISPRi knockdown of LOC646329 indicates that this lncRNA regulates cell proliferation. The discrete and abundant expression of lncRNAs among individual cells has important implications for both their biological function and utility for distinguishing neural cell types.
      datePublished:2016-04-14T00:00:00Z
      dateModified:2016-04-14T00:00:00Z
      pageStart:1
      pageEnd:17
      license:http://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/s13059-016-0932-1
      keywords:
         lncRNA
         Single-cell RNA-seq
         Developing brain
         CRISPRi
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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            name:Siyuan John Liu
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