Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA209940 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis [Illumina]
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Project description:Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis
| PRJNA209993 | ENA
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: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:The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line (control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays, Illumina microarray HT12 platform and qRT-PCR verification of targets were performed. 189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates. 3045 target genes in total were detected with 587 common and 2458 unique target genes between up and downregulated miRNAs.The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis. Comparison in triplicates the miRNA expression profile with Exiqon between human JJ012 chondrosarcoma cell line and C28 control chondrocytes
2013-08-28 | E-GEOD-48396 | biostudies-arrayexpress
Project description:The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line (control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays, Illumina microarray HT12 platform and qRT-PCR verification of targets were performed. 189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates. 3045 target genes in total were detected with 587 common and 2458 unique target genes between up and downregulated miRNAs.The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis.
2013-08-28 | GSE48396 | GEO
Project description:The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line(control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays, Illumina microarray HT12 platform and qRT-PCR verification of targets were performed.189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates.3045 target genes in total were detected woth 587 common and 2458 unique target genes between upand downregulated miRNAs. The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis.
2013-08-28 | GSE48418 | GEO
Project description:The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line(control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays, Illumina microarray HT12 platform and qRT-PCR verification of targets were performed.189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates.3045 target genes in total were detected woth 587 common and 2458 unique target genes between upand downregulated miRNAs. The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis. compare in triplicates the miRNA expression profile with Exiqon, followed by Illumina microarrays for target mRNA expression validation between human JJ012 chondrosarcoma cell l ine and C28 control chondrocytes
2013-08-28 | E-GEOD-48418 | biostudies-arrayexpress
Project description: Not available
| S-EPMC2531291 | biostudies-literature