Identification of differentially expressed lncRNAs and mRNAs in OLF
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ABSTRACT:
PROVIDER: PRJNA415999 | ENA |
REPOSITORIES: ENA
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Project description:Ossification of the ligamentum flava (OLF) is a common spinal disorder among the elderly that causes myelopathy and radiculopathy. Although studies have identified several genes that correlated with OLF, the underlying regulation network is far from clear. To identify transcriptional regulators for OLF, we compared the lncRNAs and mRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis, which revealed a panel of lncRNAs and mRNAs that were specifically regulated in ligament tissues of human undergoing ossification. To identify transcriptional regulators for OLF, we compared the lncRNAs and mRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis.
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Project description:Ossification of the ligamentum flava (OLF) is a common spinal disorder among the elderly that causes myelopathy and radiculopathy. Although studies have identified several genes that correlated with OLF, the underlying regulation network is far from clear. To identify transcriptional regulators for OLF, we compared the circRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis, which revealed a panel of circRNAs that were specifically regulated in ligament tissues of human undergoing ossification. To identify transcriptional regulators for OLF, we compared the circRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis.
2017-10-27 | GSE106255 | GEO
Project description:Ossification of the ligamentum flava (OLF) is a common spinal disorder among the elderly that causes myelopathy and radiculopathy. Although studies have identified several genes that correlated with OLF, the underlying regulation network is far from clear. To identify transcriptional regulators for OLF, we compared the microRNA expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microRNA sequencing.
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Project description:LncRNA expression profiling for liver tissues of mice fed for NFD, LSF and HSF groups Summary: An abstract of the experiment and the data analysis. Experiment Workflow: A workflow of the experiment and the data analysis. Project Description: Sample and experiment information. Array Information: Mouse 8 x 60K LncRNA expression array information. Summary Table of Files for Data Delivery: Contains summary table of files for data delivery and the recommended software programs for viewing the data. Data Analysis for LncRNAs 1. Raw LncRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity LncRNAs were filtered (LncRNAs that at least 6 out of 9 samples have flags in Present or Marginal were chosen for further analysis, these LncRNAs can be found from the LncRNA Expression Profiling Data.xls file). 2. Quality assessment of LncRNA data after filtering: Contains Box Plot and Scatter Plot for LncRNAs after filtering (This data can be found from the LncRNA Expression Profiling Data.xls file). 3. Differentially expressed LncRNAs screening: Contains differentially expressed genes with statistical significance that passed Volcano Plot filtering (Fold Change >= 2.0, P-value <= 0.05) (This data can be found from the Differentially Expressed LncRNAs.xls file). 4. Heat Map and Hierarchical Clustering: Hierarchical Clustering of Differentially Expressed LncRNAs (The heat map can be found from the LncRNA Expression Profiling Data.xls file). Data Analysis for mRNAs 1. Raw mRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity mRNAs were filtered (mRNAs that at least 6 out of 9 samples have flags in Present or Marginal were chosen for further analysis, these mRNAs can be found from the mRNA Expression Profiling Data.xls file). 2. Quality assessment of mRNA data after filtering: Contains Box Plot and Scatter Plot for mRNAs after filtering (This data can be found from the mRNA Expression Profiling Data.xls file). 3. Differentially expressed mRNAs screening: Contains differentially expressed genes with statistical significance that passed Volcano Plot filtering (Fold Change >= 2.0, P-value <= 0.05) (This data can be found from the Differentially Expressed mRNAs.xls file). 4. Heat Map and Hierarchical Clustering: Hierarchical Clustering of Differentially Expressed mRNAs (The heat map can be found from the mRNA Expression Profiling Data.xls file). 5. Pathway analysis: Pathway analysis of the differentially expressed mRNAs. 6. GO analysis: GO term analysis of the differentially expressed mRNAs. LncRNA Classification and Subgroup Analysis 1. Rinn lincRNAs profiling: Contains profiling data of all lincRNAs based on John Rinn's papers (This data can be found from the Rinn lincRNAs profiling.xls file). 2. LincRNAs nearby coding gene data table: Contains the differentially expressed lincRNAs and nearby coding gene pairs (distance < 300 kb) (This data can be found from the LincRNAs nearby coding gene data table.xls file). Sample RNA Quality Control: Sample quality control data file from NanoDrop ND-1000 spectrophotometer and standard denaturing agarose gel electrophoresis. Methods: A brief introduction of methods for sample preparation, microarray design, experiment, and data analysis.
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Project description:A total of 3,359 lncRNAs revealed by microarray analysis have been differentially expressed between the two groups, 1,995 lncRNAs identified to be up-regulated in COPD, whereas 1,364 lncRNAs have been down-regulated. Meanwhile，a total of 3,283 mRNAs have been differentially expressed, 2,589 mRNAs identified to be up-regulated in COPD, whereas 694 mRNAs were down-regulated.
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