The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells II
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ABSTRACT:
PROVIDER: PRJNA478593 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7456830_1.fastq.gz | Fastqsanger.gz | |||
| SRR7456830_2.fastq.gz | Fastqsanger.gz | |||
| SRR7456831_1.fastq.gz | Fastqsanger.gz | |||
| SRR7456831_2.fastq.gz | Fastqsanger.gz | |||
| SRR7456832_1.fastq.gz | Fastqsanger.gz |
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Project description:The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells
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Project description:The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells I
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Project description:The naive embryonic stem cells (nESCs) display unique characteristics mirroring naive pluripotency in vivo, but the molecular mechanisms underlying the self-renewal of nESCs remain incompletely understood. Here we analyzed stranded transcriptomes in mouse nESCs and epiblast-like cells (EpiLCs), and identified 135 long non-coding RNAs (lncRNAs) preferentially expressed in nESCs. We further investigated the functions of Lncenc1, a highly abundant lncRNA in mouse nESCs. Knockdown or knockout of Lncenc1 in mouse nESCs leads to significantly decreased expression of core pluripotency genes and significant reduction of colony formation capability. Furthermore, depletion of Lncenc1 down-regulates the glycolysis pathway, as indicated by significant decreases of glycolysis genes expression, glucose consumption, lactate production and Seahorse data. Mechanically, Lncenc1 associates with RNA-binding proteins PTBP1 and HNRNPK functionally. Together, we demonstrate that Lncenc1 regulates the glycolysis in mouse nESCs, suggesting novel functions of lncRNAs in linking energy metabolism and pluripotent stem cells.
2018-08-01 | GSE116462 | GEO
Project description:The naive embryonic stem cells (nESCs) display unique characteristics mirroring naive pluripotency in vivo, but the molecular mechanisms underlying the self-renewal of nESCs remain incompletely understood. Here we analyzed stranded transcriptomes in mouse nESCs and epiblast-like cells (EpiLCs), and identified 135 long non-coding RNAs (lncRNAs) preferentially expressed in nESCs. We further investigated the functions of Lncenc1, a highly abundant lncRNA in mouse nESCs. Knockdown or knockout of Lncenc1 in mouse nESCs leads to significantly decreased expression of core pluripotency genes and significant reduction of colony formation capability. Furthermore, depletion of Lncenc1 down-regulates the glycolysis pathway, as indicated by significant decreases of glycolysis genes expression, glucose consumption, lactate production and Seahorse data. Mechanically, Lncenc1 associates with RNA-binding proteins PTBP1 and HNRNPK functionally. Together, we demonstrate that Lncenc1 regulates the glycolysis in mouse nESCs, suggesting novel functions of lncRNAs in linking energy metabolism and pluripotent stem cells.
2018-08-01 | GSE116458 | GEO
Project description:Here we propose a set of molecular criteria for evaluating the naive human pluripotent state. We show by RNA-seq that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. RNA-seq of 4 naive ES samples in 4i/LA, 3 naive ES samples in 5i/LA, 2 transgene-dependant naive ES cell samples, and 5 primed ES cell samples (in hESM)
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Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal.
2. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in diagnosis of colorectal cancer patients & its relation to tumor staging.
3. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in precancerous colorectal diseases.
4. Compare long noncoding RNA (CCAT1) expression with traditional marker; carcinoembryonic antigen (CEA) and Carbohydrate antigen 19-9 (CA19-9) in diagnosis of colorectal cancer.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2018-08-01 | GSE116602 | GEO
Project description:Here we propose a set of molecular criteria for evaluating the naive human pluripotent state. We show by RNA-seq that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. RNA-seq of 3 naive ES samples in NHSM (Gafni et al.) and 3 primed ES cell samples (in hESM)
2016-08-16 | E-GEOD-85689 | biostudies-arrayexpress
Project description:We employed whole-genome RNA-sequencing to profile mRNAs and both annotated and novel long noncoding RNAs (lncRNAs) in human naive, central memory, and effector memory CD4+ T cells. Loci transcribing both lineage-specific annotated and novel lncRNA are adjacent to lineage-specific protein-coding genes in the genome. Lineage-specific novel lncRNA loci are transcribed from lineage-specific typical- and supertranscriptional enhancers and are not multiexonic, thus are more similar to enhancer RNAs. Novel enhancer-associated lncRNAs transcribed from the IFNG locus bind the transcription factor NF-κB and enhance binding of NF-κB to the IFNG genomic locus. Depletion of the annotated lncRNA, IFNG-AS1, or one IFNG enhancer-associated lncRNA abrogates IFNG expression by memory T cells, indicating these lncRNAs have biologic function.
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Project description:Long noncoding RNAs (lncRNAs) have emerged as important regulators of diverse cellular processes, but their roles in the developing immune system are poorly understood. In this study, we analysed lncRNA expression during human B-cell development by array-based expression profiling of eleven distinct flow-sorted B-cell subsets, comprising pre-B1, pre-B2, immature, naive, memory, and plasma cells from bone marrow biopsies (n=7), and naive, centroblast, centrocyte, memory, and plasmablast cells from tonsil tissue samples (n=6), respectively. A remapping strategy was used to assign the array probes to 37630 gene-level probe sets, reflecting the most recent updates in genomic and transcriptomic databases, which enabled expression profiling of 19579 long noncoding RNAs, comprising 3947 antisense RNAs, 5277 lincRNAs, 7625 pseudogenes, and 2730 additional lncRNAs. As a first step towards inferring the functions of the identified lncRNAs in developing B-cells, we analysed their co-expression with well-characterized protein-coding genes, a method known as â??guilt by associationâ??. By using weighted gene co-expression network analysis, we identified 272 lincRNAs, 471 antisense RNAs, 376 pseudogene RNAs, and 64 lncRNAs within seven sub-networks associated with distinct stages of B-cell development, such as early B-cell development, B-cell proliferation, affinity maturation of antibody, and terminal differentiation. These data provide an important resource for future studies on the functions of lncRNAs in development of the adaptive immune response, and the pathogenesis of B-cell malignancies that originate from distinct B-cell subpopulations. Tonsils were collected from six patients (homo sapiens) during routine tonsillectomy. Mononuclear cells were isolated from tonsils and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of naive, centroblasts, centrocytes, menory and plasmablast cells were isolated and a total of 30 gene expression profiles were generated using the HuEx-1_0-st-v2-micro array chip from Affymetrix.
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