Ontology highlight
ABSTRACT:
PROVIDER: PRJNA258590 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (miRNA)
| PRJNA259359 | ENA
Project description:The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (mRNA)
| PRJNA259358 | ENA
Project description:Model destription:
The model describes the stochastic dynamics of two variables, protein and mRNA of a gene with constitutive expression.
Publication:
A New Efficient Approach to Fit Stochastic Models on the Basis of High-throughput Experimental Data Using a Model of IRF7 Gene Expression as Case Study
Authors
Luis U. Aguilera, Christoph Zimmer and Ursula Kummer.
2017-03-17 | MODEL1608100000 | BioModels
Project description:The experiment aims to identify regulatory miRNA networks influencing mRNA profiles in oral lichen planus (OLP). RNA and miRNA were extracted simultaniously using miRVana (Ambion, Life Technologies). Sample and array processing was carried out according to the manufacturer's guidelines. Affymetrix raw data was processed using AGCC Expression Console 1.1 (Affymetrix), employing RMA normalization. Linking miRNA and mRNA was performed with a correlation analysis, while a false discovery rate was used to exclude false-positive correlations between miRNAs and their predicted targets.
2013-05-06 | GSE38616 | GEO
Project description:The experiment aims to identify regulatory miRNA networks influencing mRNA profiles in oral lichen planus (OLP). RNA and miRNA were extracted simultaniously using miRVana (Ambion, Life Technologies). Sample and array processing was carried out according to the manufacturer's guidelines. Affymetrix raw data was processed using AGCC Expression Console 1.1 (Affymetrix), employing RMA normalization. Linking miRNA and mRNA was performed with a correlation analysis, while a false discovery rate was used to exclude false-positive correlations between miRNAs and their predicted targets.
2013-05-06 | GSE38615 | GEO
Project description:The experiment aims to identify regulatory miRNA networks influencing mRNA profiles in oral lichen planus (OLP). RNA and miRNA were extracted simultaniously using miRVana (Ambion, Life Technologies). Sample and array processing was carried out according to the manufacturer's guidelines. Affymetrix raw data was processed using AGCC Expression Console 1.1 (Affymetrix), employing RMA normalization. Linking miRNA and mRNA was performed with a correlation analysis, while a false discovery rate was used to exclude false-positive correlations between miRNAs and their predicted targets. 7 cases (OLP) and 7 controls (healthy individuals). Genome wide mRNA and miRNA screening, linking both datasets (see summary).
2013-05-06 | E-GEOD-38615 | biostudies-arrayexpress
Project description:The experiment aims to identify regulatory miRNA networks influencing mRNA profiles in oral lichen planus (OLP). RNA and miRNA were extracted simultaneously using miRVana (Ambion, Life Technologies). Sample and array processing was carried out according to the manufacturer's guidelines. Affymetrix raw data was processed using AGCC Expression Console 1.1 (Affymetrix), employing RMA normalization. Linking miRNA and mRNA was performed with a correlation analysis, while a false discovery rate was used to exclude false-positive correlations between miRNAs and their predicted targets. 7 cases (OLP) and 7 controls (healthy individuals). Genome wide mRNA and miRNA screening, linking both datasets (see summary).
2013-05-06 | E-GEOD-38616 | biostudies-arrayexpress
Project description:In the present study, we used a high-throughput small RNA deep sequencing followed by a systematic computational analysis to identify genome wide mutant p53R273H regulated miRNAs in both DNA damage dependent and independent context. Several miRNA-mRNA regulatory networks have been predicted that might contribute to mutant p53 GOF properties. Differentially regulated miRNA signature profile has been validated in the lung cancer patients harboring wildtype and mutant p53. We identified specific miRNA signatures for lymph node metastasis associated with p53 mutation in lung adenocarcinoma and also predicted the possible contribution of two mutant p53 regulated miRNAs in EMT process. Furthermore, this study identified a hitherto unknown miRNA in human which might act as one of the crucial downstream targets of GOF mutant p53 to confer oncogenic properties. Determination of mutant p53R273H regulated microRNAs H1299 cells.
2017-04-28 | E-GEOD-68353 | biostudies-arrayexpress
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. Our maps of nucleotide flexibility enable making predictions about the establishment of protein-rRNA interactions, providing intriguing insights into the temporal order of protein-rRNA as well as long-range inter-domain rRNA interactions. These data argue that many distant domains in the rRNA can assemble simultaneously during early 60S assembly and underscore the enormous complexity of 60S synthesis.Ribosome biogenesis is a dynamic process that involves the ordered assembly of ribosomal proteins and numerous RNA structural rearrangements. Here the authors apply ChemModSeq, a high-throughput RNA structure probing method, to quantitatively measure changes in RNA flexibility during the nucleolar stages of 60S assembly in yeast.
2017-10-04 | GSE83821 | GEO