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    Results: 20

    1.

    lincRNAs act in the circuitry controlling pluripotency and differentiation

    (Submitter supplied) While thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem cells (ESC) and characterized the effects on gene expression. Here we show that knockdown of lincRNAs have major consequences on gene expression patterns, comparable to knockdown of well-known ESC regulators. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array; Non-coding RNA profiling by array
    Platform:
    GPL13767
    449 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE30245
    ID:
    200030245
    2.

    Many Human Large Intergenic Non-coding RNAs Associate with Chromatin Modifying Complexes and Affect Gene Expression

    (Submitter supplied) We recently showed that the mammalian genome encodes more than a thousand large intergenic non-coding RNAs (lincRNAs) that are clearly conserved across mammals and thus functional. Gene expression patterns have implicated these lincRNAs in diverse biological processes including cell cycle regulation, immune surveillance, and embryonic stem cell pluripotency. However, the mechanism by which these lincRNAs function is unknown. more...
    Organism:
    Homo sapiens
    Type:
    Non-coding RNA profiling by genome tiling array; Expression profiling by array
    Platforms:
    GPL8792 GPL570 GPL8791
    68 Samples
    Download data:
    GEO (CEL, GFF)
    Series
    Accession:
    GSE16226
    ID:
    200016226
    3.

    Large intergenic non-coding RNAs as novel modulators of reprogramming

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array; Non-coding RNA profiling by genome tiling array
    Platforms:
    GPL8792 GPL8791 GPL570
    43 Samples
    Download data:
    GEO (CEL, GFF)
    Series
    Accession:
    GSE24182
    ID:
    200024182
    4.

    Large intergenic non-coding RNAs as novel modulators of reprogramming: human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells (LincRNA expression)

    (Submitter supplied) Expression profiling of non coding RNAs using tilling arrays from ES, Fibroblasts and Fibroblasts derived iPSC LincRNA profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells
    Organism:
    Homo sapiens
    Type:
    Non-coding RNA profiling by genome tiling array
    Platform:
    GPL8791
    14 Samples
    Download data:
    GEO (GFF)
    Series
    Accession:
    GSE24181
    ID:
    200024181
    5.

    Large intergenic non-coding RNAs as novel modulators of reprogramming: siRNA (gene expression)

    (Submitter supplied) lincRNA-ST8SIA3 was depleted using siRNAs and associated gene expression changes were profiled on Affymentrix arrays
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL570
    7 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE23973
    ID:
    200023973
    6.

    Large intergenic non-coding RNAs as novel modulators of reprogramming: human embryonic stem cells, CD34+ cells, and CD34+ derived induced pluripotent stem cells (LincRNA expression)

    (Submitter supplied) LincRNA expression profiles of human embryonic stem cells, CD34+ cells, and CD34+ derived induced pluripotent stem cells
    Organism:
    Homo sapiens
    Type:
    Non-coding RNA profiling by genome tiling array
    Platform:
    GPL8792
    8 Samples
    Download data:
    GEO (GFF)
    Series
    Accession:
    GSE23970
    ID:
    200023970
    7.

    Large intergenic non-coding RNAs as novel modulators of reprogramming: ESCs, fibroblast, and fibroblast-derived iPSC (gene expression)

    (Submitter supplied) Gene expression profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL570
    14 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE23968
    ID:
    200023968
    8.

    lincRNA Expression

    (Submitter supplied) There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. While there are some well-characterized examples, the vast majority (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here, we report a new approach to identifying large non-coding RNAs (ncRNAs) by using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci. more...
    Organism:
    Mus musculus
    Type:
    Non-coding RNA profiling by genome tiling array; Expression profiling by array
    6 related Platforms
    66 Samples
    Download data:
    GEO (CEL, GFF)
    Series
    Accession:
    GSE13765
    ID:
    200013765
    9.

    A central role for TFIID in the pluripotent transcription circuitry

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Platform:
    GPL13383
    14 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE33646
    ID:
    200033646
    10.

    A central role for TFIID in the pluripotent transcription circuitry [PP003]

    (Submitter supplied) Pluripotent stem cells can be isolated from early embryos or induced by cell fusion, somatic nuclear transfer, or expression of a selected set of transcription factors. Embryonic stem (ES) cells are characterized by an open chromatin configuration and high transcription levels achieved via autoregulatory and feed-forward transcription factor loops. How the general transcription machinery is involved in pluripotency is unclear. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Platform:
    GPL13383
    6 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE33645
    ID:
    200033645
    11.

    A central role for TFIID in the pluripotent transcription circuitry [PP002]

    (Submitter supplied) Pluripotent stem cells can be isolated from early embryos or induced by cell fusion, somatic nuclear transfer, or expression of a selected set of transcription factors. Embryonic stem (ES) cells are characterized by an open chromatin configuration and high transcription levels achieved via autoregulatory and feed-forward transcription factor loops. How the general transcription machinery is involved in pluripotency is unclear. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Platform:
    GPL13383
    8 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE33644
    ID:
    200033644
    12.

    ChIP-chip of siGFP- or siHOTTIP-treated foreskin fibroblasts with anti-H3K4me3, anti-H3K27me3, anti-H3K4me2, anti-histone, anti-MLL1, and anti-WDR5 antibodies on HOX tiling array

    (Submitter supplied) Coordinate loss of MLL1 and WDR5 occupancy caused by HOTTIP knockdown were observed in distal HOXA genes. These regions correspondingly lost H3K4me3 and H3K4me2, without changes in pan-histone or H3K27me3. human foreskin fibroblasts (CRL2091), anti-H3K4me3 (Abcam ab8580, lot#1016899), anti-H3K4me2 (Abcam ab32356, lot#947550), anti-H3K27me3 (Abcam ab4729, lot#1021724), anti-histone H3 (Abcam ab1791, lot#1025144), anti-MLL1 (gift of R. more...
    Organism:
    Homo sapiens
    Type:
    Genome binding/occupancy profiling by genome tiling array
    Platform:
    GPL5790
    14 Samples
    Download data:
    GEO (GFF, PAIR)
    Series
    Accession:
    GSE26540
    ID:
    200026540
    13.

    Transcriptome Analysis of LincRNA TUNA Knockdown in Mouse Embryonic Stem Cells

    (Submitter supplied) Globel gene expression was analyzed by RNA-seq to study the role of lincRNA TUNA in pluripotent mouse embryonic stem cells.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL13112
    12 Samples
    Download data:
    GEO (TXT), SRA SRP022177
    Series
    Accession:
    GSE46730
    ID:
    200046730
    14.

    ChIP-chip for histone modifications in hESCs and differentiated hESCs

    (Submitter supplied) The objective of this study was to identify how histone modifications are differentially marked at promoter and enhancer elements in hESCs before and after differentiation to understand the regulatory mechanisms that defined pluripotency and early differentiation.
    Organism:
    Homo sapiens
    Type:
    Genome binding/occupancy profiling by genome tiling array
    29 related Platforms
    94 Samples
    Download data:
    GEO (CEL, GFF, PAIR)
    Series
    Accession:
    GSE30434
    ID:
    200030434
    15.

    Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution

    (Submitter supplied) Thousands of large intervening non-coding RNAs (lincRNAs) have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs, we used chromatin marks, poly(A)-site mapping and RNA-Seq data, to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs, only 29 had detectable sequence similarity with putative mammalian orthologs, typically restricted to a single short region of high conservation. more...
    Organism:
    Danio rerio
    Type:
    Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL9319
    16 Samples
    Download data:
    GEO (BAM, BED, BW), SRA SRP008845
    Series
    Accession:
    GSE32880
    ID:
    200032880
    16.

    Human embryonic stem cells

    (Submitter supplied) Undifferentiated human embryonic stem cells grown on mouse embryonic fibroblast feeder layers. HES3 and HES4 are proprietary human ES cell lines of ES Cell International Pte Ltd. Singapore. Keywords: other
    Organism:
    Homo sapiens
    Type:
    Expression profiling by SAGE
    Platform:
    GPL4
    2 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE608
    ID:
    200000608
    17.

    BAF 250 ko ES cells series

    (Submitter supplied) To study the function of BAF250 during ES cell self renewal and differentiation Keywords: gene expression comparison between heterozygous,homozygoous and wild type ES cells
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Dataset:
    GDS3387
    Platform:
    GPL1261
    4 Samples
    Download data:
    GEO (CEL, CHP)
    Series
    Accession:
    GSE10553
    ID:
    200010553
    18.
    Full record GDS3387

    Chromatin remodeling component BAF250a deficiency effect on embryonic stem cells in vitro

    Analysis of embryonic stem (ES) cells deleted for BAF250a in vitro. BAF250 is a component of the BAF chromatin remodeling complex. Results provide insight into the role of BAF250a in ES cell self-renewal and differentiation.
    Organism:
    Mus musculus
    Type:
    Expression profiling by array, count, 3 genotype/variation sets
    Platform:
    GPL1261
    Series:
    GSE10553
    4 Samples
    Download data:
    GEO (CEL, CHP)
    19.

    A genome wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation

    (Submitter supplied) Despite intense investigation of intrinsic and extrinsic factors that regulate pluripotency, the process of initial fate commitment of embryonic stem (ES) cells is still poorly understood. Here, we used a genome wide shRNA screen in mouse ES cells to identify genes that are essential for initiation of differentiation. Knockdown of the scaffolding protein Mek binding protein 1 (Mp1, also known as Lamtor3, Map2k1ip1) stimulated self-renewal of ES cells, blocked differentiation and promoted proliferation. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Platform:
    GPL6887
    8 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE32595
    ID:
    200032595
    20.

    Integrative Annotation of Human Large Intergenic Non-Coding RNAs Reveals Global Properties and Specific Subclasses

    (Submitter supplied) Large intergenic non-coding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-Seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalogue of over 8,000 human lincRNAs. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL9115
    9 Samples
    Download data:
    GEO (BAM), SRA SRP007494
    Series
    Accession:
    GSE30554
    ID:
    200030554

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