Assessment of NanoString technology as a tool for profiling circulating miRNA in maternal blood during pregnancy
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PROVIDER: PRJNA1109349 | ENA |
REPOSITORIES: ENA
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Project description:Circulating maternal miRNA is a promising source of biomarkers for antenatal diagnostics. The hybridisation-based NanoString nCounter is a popular global screening tool due to its simplicity and ease-of-use but there is a lack of standardisation in analysis methods. In this study we used a rodent model to examine the effect of user-defined variables within the data processing software nSolver upon reported changes in maternal blood miRNA during pregnancy. These included the choice of normalisation and background correction methods as well as the background threshold applied. Our results suggest that these variables greatly influence the output of the nSolver software. Changes in a total of 31 miRNAs were detected, but many of these were only picked up by a single combination of analysis variables and no reported change was common to all. RT-qPCR validated changes in 4 miRNAs with known roles in pregnancy (miR-183, miR-196c, miR-431, miR-450a) from a panel of 14 candidates in which changes were supported by multiple analysis workflows. No single nSolver analysis workflow had successfully identified all four validated changes. We then reverse-engineered the nSolver analysis to further investigate the effect of each step in the analysis upon the count data. Our results highlight the need for standardised nCounter data analysis methods and detailed reporting of these methods in papers. We suggest that robust data can only be obtained by examining multiple analysis workflows.
2024-09-03 | GSE267016 | GEO
Project description:AimCirculating maternal MicroRNA (miRNA) is a promising source of biomarkers for antenatal diagnostics. NanoString nCounter is a popular global screening tool due to its simplicity and ease of use, but there is a lack of standardisation in analysis methods. We examined the effect of user-defined variables upon reported changes in maternal blood miRNA during pregnancy.MethodsTotal RNA was prepared from the maternal blood of pregnant and control rats. miRNA expression was profiled using Nanostring nCounter. Raw count data were processed using nSolver using different combinations of normalisation and background correction methods as well as various background thresholds. A panel of 14 candidates in which changes were supported by multiple analysis workflows was selected for validation by RT-qPCR. We then reverse-engineered the nSolver analysis to gain further insight.ResultsThirty-one putative differentially expressed miRNAs were identified by nSolver. However, each analysis workflow produced a different set of reported biomarkers and none of them was common to all analysis methods. Four miRNAs with known roles in pregnancy (miR-183, miR-196c, miR-431, miR-450a) were validated. No single nSolver analysis workflow could successfully identify all four validated changes. Reverse engineering revealed errors in nSolver data processing which compound the inherent problems associated with background correction and normalisation.ConclusionOur results suggest that user-defined variables greatly influence the output of the assay. This highlights the need for standardised nSolver data analysis methods and detailed reporting of these methods. We suggest that investigators in the future should not rely on a single analysis method to identify changes and should always validate screening results.
| S-EPMC11648433 | biostudies-literature
Project description:Tissue samples were harvested with the Keyes biopsy punch (8 mm; manufactured by HNM) from the caudal edge of the right superficial pectoral muscle perpendicular to myofibers and to the keel bone. Total RNA was isolated from p. major samples using mirVana™ miRNA Isolation Kit. Quality checks were performed by measuring the concentration and “RNA Integrity Number” of individual RNA samples using NanoDrop 1000 and Agilent Bioanalyzer 2100. The RNA samples were normalized and sent to NanoString Inc. (Seattle, WA, USA) for the quantification of gene expression levels using NanoString nCounter® technology. For this, 192 target genes, along with 12 housekeeping genes were selected based on multiple RNA-seq experiments conducted in our laboratories.
2021-01-11 | GSE162634 | GEO
Project description:Although rescue of the corpus luteum is required for pregnancy, luteal function during maternal recognition of pregnancy remains largely unexplored. CL were collected from pregnant cattle on days 14, 17, 20, and 23, to encompass the maternal recognition of pregnancy period. Nanostring technology was used to profile miRNA. A total of 27 miRNA changed. MiRNA that increased were predicted to inhibit phosphatidylinositol signaling, while those that decreased may be negative regulators of steroidogenesis. Overall, these data indicate that there are changes in the CL of pregnancy that are important for continued luteal function.
2020-03-28 | GSE147623 | GEO
Project description:Gene expression analysis of chicken p. major muscle using the NanoString nCounter technology
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Project description:Targeted transcriptomic analysis of pancreatic adenocarcinoma in EUS-FNA samples by NanoString technology
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Project description:Gene expression profiling of newly-diagnosed DLBCL samples with the NanoString nCounter technology
| PRJNA738873 | ENA
Project description:Poor reproductive performance remains a major issue in the dairy industry, with extremely low calving rates (34 %) affecting milk production, profitability and the economy in general. Early pregnancy detection can help identify non-pregnant animals within three weeks of insemination, minimizing delays and shortening calving intervals. However current pregnancy detection methods are not accurate enough to support such reproductive management programs. MiRNAs have been proposed as non-invasive biomarkers of pregnancy and several reproductive diseases in humans. We previously identified miR-26a as a potential early pregnancy biomarker in cattle. In the current study, using miRNA sequencing, we identified and validated differentially expressed miRNAs on Day 60 of pregnancy compared to Day 0 (non-pregnant), and we investigated the expression of these validated miRNAs in early pregnancy aiming to identify additional early pregnancy biomarker candidates. The expression levels of selected miRNAs which are differentially expressed during pregnancy will also be investigated as part of this study.
2017-03-21 | GSE83509 | GEO
Project description:The current study makes use of NanoString targeted technology to profile urinary exosomal miRNAs from IgA nephropathy affected patients and corresponding healthy controls. Circulatory biomarkers were detected for IgA nephropathy from Indian cohort which can be made used for the diagnostic therapy. 14 miRNAs were detected to be related to the disregulation in miRNome of IgA nephropathy patients using lasso feature selection method, out of which multiple miRNAs like hsa.mir.146b.3p, hsa.mir.599 and many more was resulted with high AUROC values >=0.9 efficient in differentiating between healthy controls and IgA nephropathy condition. These markers can be use further in the diagnosis and treatment of IgAN.
2023-12-13 | GSE244625 | GEO
Project description:Although rescue of the corpus luteum is required for pregnancy, luteal function during maternal recognition of pregnancy remains largely unexplored. CL were collected from pregnant cattle on days 14, 17, 20, and 23, to encompass the maternal recognition of pregnancy period. Next Generation Sequencing was used to profile mRNA abundance during this time, while tandem mass spectrometry and Nanostring technology were used to profile proteins and miRNA, respectively. A total of 1157 mRNA were differentially abundant. mRNA that increased were regulators of interferon signaling and DNA repair, while those that decreased were associated with luteolytic processes, such as calcium signaling and matrix metallopeptidase (MMP) signaling, indicating inhibition of these processes. mRNA that were maximally abundant on day 20 were primarily associated with immune processes. Overall, these data indicate that there are changes in the CL of pregnancy that are important for continued luteal function.
2020-03-28 | GSE147630 | GEO