{"id":2853,"date":"2023-06-14T10:09:29","date_gmt":"2023-06-14T09:09:29","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&p=2853"},"modified":"2023-06-16T09:11:39","modified_gmt":"2023-06-16T08:11:39","slug":"different-approaches-in-microrna-analysis","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/different-approaches-in-microrna-analysis\/","title":{"rendered":"Different approaches in microRNA analysis"},"content":{"rendered":"\n

Barbara Jenko Bizjan1, 2*<\/sup>, Bine Stan\u010di\u010d1<\/sup>, Iva Saboli\u01073<\/sup>, Maja \u0160talekar1<\/sup> and Ur\u0161ula Prosenc Zmrzljak1<\/sup><\/p>\n\n\n\n

1<\/sup>BIA Separations CRO, Labena d.o.o., Ljubljana, Slovenia<\/p>\n\n\n\n

2<\/sup>Clinical Institute of Special Laboratory Diagnostics, University Children\u2019s Hospital, UMC, Ljubljana, Slovenia<\/p>\n\n\n\n

3<\/sup>eDNA labs, Labena d.o.o., Zagreb, Croatia<\/p>\n\n\n\n

barbara.jenko [at] biaseparationscro.com<\/p>\n\n\n\n

Abstract<\/strong><\/p>\n\n\n\n

Background: microRNA might serve as a predictive biomarker for treatment response in stem cell treatment in knee osteoarthritis. Different sample types are going to be collected to enlighten the true biological role. MicroRNA analysis necessitates diverse approaches based on the sample type. In this study, we examined microRNA profiles in plasma samples, synovial fluid, and adipose-derived fat tissue. We conducted a comparative analysis of different microRNA analysis methods to assess the data.<\/p>\n\n\n\n

Methods: The first approach involved a series of steps, including adapter trimming, quality filtering, size filtering, and mapping of all reads to the human reference genome (GRCh38.p12). Subsequently, genome-mapped reads were aligned to known miRNA sequences from miRBase. Reads that did not match miRNAs were subjected to further classification using additional databases, such as RNAcentral. The second pipeline also encompassed adapter trimming, quality filtering, and size filtering. Additionally, it involved collapsing individual reads into repeat sequences, followed by alignment to the mature index of miRBase. Unaligned reads were classified as isomiRs based on their alignment to the hairpin index of miRBase.<\/p>\n\n\n\n

Results: We processed sequences from three plasma samples, three adipose fat tissue samples, and three synovial fluid samples. Although there were slight variations in microRNA read counts, the average ratio between counts was 0.92 (SD=0.29). Notably, the second pipeline yielded higher read counts compared to the first pipeline.<\/p>\n\n\n\n

Conclusion: The results obtained from both microRNA bioinformatic pipelines demonstrated similar outcomes, suggesting that the choice of pipeline is unlikely to have a significant impact on the derived biological insights.<\/p>\n\n\n\n

Keywords:<\/strong> bioinformatics, microRNA, sequencing<\/p>\n\n\n\n

Funding:<\/strong> This work was performed as a part of project: \u201cDevelopment of advanced prediction tool for successful and optimized treatment course in pathological joint changes based on quantification of inflammatory biomarkers \u2013 PredicTest\u201d which is co-funded by EUREKA member countries and the European Union Horizon 2020 Framework Programme<\/p>\n","protected":false},"excerpt":{"rendered":"

Barbara Jenko Bizjan1, 2*<\/sup>, Bine Stan\u010di\u010d1<\/sup>, Iva Saboli\u01073<\/sup>, Maja \u0160talekar1<\/sup> and Ur\u0161ula Prosenc Zmrzljak1<\/sup><\/p>\n

1<\/sup>BIA Separations CRO, Labena d.o.o., Ljubljana, Slovenia<\/p>\n

2<\/sup>Clinical Institute of Special Laboratory Diagnostics, University Children\u2019s Hospital, UMC, Ljubljana, Slovenia<\/p>\n

3<\/sup>eDNA labs, Labena d.o.o., Zagreb, Croatia<\/p>\n

Continue reading<\/span><\/i><\/a> <\/p>\n","protected":false},"author":162,"featured_media":0,"template":"","categories":[8],"tags":[],"yoast_head":"\nDifferent approaches in microRNA analysis - BelBi 2023<\/title>\n<meta name=\"robots\" content=\"noindex, follow\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Different approaches in microRNA analysis - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"Barbara Jenko Bizjan1, 2*, Bine Stan\u010di\u010d1, Iva Saboli\u01073, Maja \u0160talekar1 and Ur\u0161ula Prosenc Zmrzljak11BIA Separations CRO, Labena d.o.o., Ljubljana, Slovenia2Clinical Institute of Special Laboratory Diagnostics, University Children\u2019s Hospital, UMC, Ljubljana, Slovenia3eDNA labs, Labena d.o.o., Zagreb, Croatia Continue reading\" \/>\n<meta property=\"og:url\" content=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/different-approaches-in-microrna-analysis\/\" \/>\n<meta property=\"og:site_name\" content=\"BelBi 2023\" \/>\n<meta property=\"article:modified_time\" content=\"2023-06-16T08:11:39+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/different-approaches-in-microrna-analysis\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/different-approaches-in-microrna-analysis\/\",\"name\":\"Different approaches in microRNA analysis - 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