Project description:We have investigated the effect of exposure to 150 mg/kg benzo(a)pyrene (BaP) for 3 days on mRNA and miRNA expression levels in adult mouse liver. We used Agilent miRNA array platforms to assess effects of BaP exposure on miRNA expression levels. Our results indicate a distinct lack of effect of BaP of miRNA expression, despite widespread changes in mRNA levels. The data in the attached array files were used a positive control for the Agilent platform, to indicate that the platform was able to detect significant differences in abundance of miRNA between two samples with great differences in miRNA content. Keywords: Toxicology, miRNA
Project description:In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides array Comparative Genomics Hybridization (aCGH, Agilent) , we used a commerical SNP-array (Illumina) including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.
Project description:To determine the differential miRNA levels in heroin addicts, we comparatively profiled plasma miRNA expression of heroin abusers and healthy controls using Agilent Human miRNA Array.
Project description:To determine the differential miRNA levels in methamphetamine addicts, we comparatively profiled plasma miRNA expression of methamphetamine abusers and healthy controls using Agilent Human miRNA Array.
Project description:In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides snp-array, we used a customized array Comparative Genomics Hybridization (aCGH, Agilent) approach for a cohort of clinical samples including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.
Project description:Purpose: to detect the expression differences of miRNAs in exosomes derived from HOTTIP-overexpressed and NC FaDu cells Methods: Total RNA containing small RNA was extracted from oe-HOTTIP FaDu-derived exosomes. Use Agilent miRNA array for miRNA analysis. Each slide of the Agilent array is designed as eight identical arrays (8×60K format), and each array contains probes for detecting 2549 human mature miRNAs from miRBase R21.0. Each miRNA was repeatedly detected by the probe 30 times. The array also contains 2164 Agilent control probes. GeneSpring software V13 (Agilent) was used to analyze the miRNA array data for data aggregation, standardization and quality control. Perform the default 90th percentile normalization method for date preprocessing. To select differentially expressed genes, we used thresholds of ≥2 and ≤−2 fold change, and the Benjamini-Hochberg corrected p vlaue was 0.05. Results: The expression of 5000 miRNAs were tested and 257 miRNAs were significantly down-regulated. Conclusion: 257 down-regulated miRNAs were candidates for HOTTIP-associated ceRNA network
