Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA357108 | ENA |
REPOSITORIES: ENA
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Project description:Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture
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Project description:Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture (mouse)
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Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression.
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Project description:Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs.
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Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes
2014-08-06 | GSE58734 | GEO
Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression. Two-condition experiment, Normoxic MSCs vs. Hypoxic MSCs.
2011-02-19 | E-GEOD-20463 | biostudies-arrayexpress
Project description:Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and consecutive disease. However, the prediction of such effects remains a challenge. Here we present a polymer physics based approach (PRISMR) to model chromatin folding and to predict enhancer-promoter contacts. Using the Epha4 locus as a model, the effects of pathogenic SVs were predicted in-silico and compared to published Hi-C and capture Hi-C data generated from mouse limb buds and patient-derived fibroblasts. PRISMR deconvolutes the folding complexity of the studied locus, and identifies SV-induced alterations of 3D genome organization in the homozygous as well as the heterozygous state. Our method accurately predicts the specific sites of ectopic chromatin contacts that produce extensive rewiring of regulatory interactions, causing disease by gene misexpression. PRISMR can be used to predict interactions in silico thereby providing a tool for analyzing the disease causing potential of SVs.
2018-02-12 | GSE92291 | GEO
Project description:Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and consecutive disease. However, the prediction of such effects remains a challenge. Here we present a polymer physics based approach (PRISMR) to model chromatin folding and to predict enhancer-promoter contacts. Using the Epha4 locus as a model, the effects of pathogenic SVs were predicted in-silico and compared to published Hi-C and capture Hi-C data generated from mouse limb buds and patient-derived fibroblasts. PRISMR deconvolutes the folding complexity of the studied locus, and identifies SV-induced alterations of 3D genome organization in the homozygous as well as the heterozygous state. Our method accurately predicts the specific sites of ectopic chromatin contacts that produce extensive rewiring of regulatory interactions, causing disease by gene misexpression. PRISMR can be used to predict interactions in silico thereby providing a tool for analyzing the disease causing potential of SVs.
2018-02-12 | GSE92290 | GEO
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes Sequence library of miRNAs from a single sample of human foetal mesenchymal stem cells. Results tested and confirmed by northern blotting. Please note that only raw data files are available for the embryonic and neual samples and thus, directly submitted to SRA (SRX547311, SRX548700, respectively under SRP042115/PRJNA247767)
2014-08-06 | E-GEOD-58734 | biostudies-arrayexpress
Project description:Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs. Two-condition experiment, KP MSCs vs. 3A6 MSCs.
2011-08-24 | E-GEOD-23936 | biostudies-arrayexpress