Small non-coding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology Small non-coding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology snd1150-1-1.0 https://doi.org/10.5878/c1mq-9r62 Swedish National Data Service Svensk nationell datatjänst Landing page Small non-coding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology Small non-coding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology snd1150-1-1.0 https://doi.org/10.5878/c1mq-9r62 10.1101/2020.05.15.097519 oai:swepub.ki.se:462651 10.1073/pnas.2011574118 urn:nbn:se:su:diva-193708 Zheleznyakova, Galina Zheleznyakova, Galina Piket, Eliane Piket, Eliane Needhamsen, Maria Needhamsen, Maria Jagodic, Maja Jagodic, Maja 2017-00777_VR 2017-00777_VR 2018-02638_VR 2018-02638_VR 2014-03124_VR 2014-03124_VR Swedish National Data Service Svensk nationell datatjänst Landing page Multiple Sclerosis Multipel skleros Multiple Sclerosis, Relapsing-Remitting Remitterande multipel skleros To improve our understanding of MS pathology and heterogeneity and provide new strategies for biomarkers and treatments development we carried out a genome-wide small non-coding RNA analysis. The analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. We aimed to detect differentially expressed small non-coding RNAs between MS and controls. The data contains unique molecular identifier (UMI) count information for each transcript. The small non-coding RNA analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. One INDC control was missing a CSF cell and cell-free CSF sample and one NINDC control was missing a PBMC and plasma sample. Small non-coding RNAs were isolated from 300 ul of plasma or CSF using the miRCURY RNA isolation kit for biofluids (Exiqon, Denmark) or from CSF cells and peripheral blood mononuclear cells precipitate using the miRNAeasy micro kit (Qiagen, Germany). Small non-coding RNA libraries were prepared as previously described at PMID: 27798564. The libraries were sequenced on eight lanes of HiSeq2500. Preprocessing and alignment were done according to PMID: 30250291. The "Unique molecular identifier_sncRNAs_analysis_MS" file contains unique molecular identifier count information for each small non-coding RNA transcript as well as other types of transcripts identified in the sequencing libraries from 44 individuals and 4 compartments (PBMCs, CSF cells, plasma, cell-free CSF). Altogether 176 samples. The metafile contains information about the disease status, sex, age for all MS patients and controls. The "readme" explains the contents of the data files and contains the variables list. Små icke-kodade RNA (sncRNA) spelar en viktig roll i regleringen av olika processer i kroppen, särskilt i immunsystemet och kan lätt detekteras i kroppsvätskor. Projektets specifika syfte är att genomföra screening av små-icke-kodande RNA från perifert blod och cerebrospinalvätska hos MS-patienter i syfte att avslöja deras biologiska roll i MS och testa deras potential som nya MS-biomarkörer. Vi analyserade förändringarna i nivån av sncRNA i blod och cerebrospinalvätska hos patienter med MS (29) och kontroller (16). Patienter med olika former av MS inkluderades i analysen för att klargöra mekanismerna genom vilka sncRNA kan bidra till utvecklingen av en viss form av sjukdomen. Uppgifterna innehåller råinformation om molekyler för varje transkript. För mer information se den engelska katalogsidan https://snd.gu.se/en/catalogue/study/SND1150 Sweden Sverige IndividualIndividual IndividIndivid CellsCells CellerCeller Multiple Sclerosis patients (29), non-inflammatory neurological disease patients (11), Systemic lupus erythematosus patients (5) Patienter med Multipel skleros (29), Kontroller (16) Numeric Text Non-probabilityNon-probability Icke-sannolikhetsurvalIcke-sannolikhetsurval Focus groupFocus group FokusgruppFokusgrupp Access to data through SND. Data are freely accessible. Åtkomst till data via SND. Data är fritt tillgängliga. openAccess Profiling of small non-coding RNAs across cellular and biofluid compartments: implications for multiple sclerosis immunopathology. Galina Yurevna Zheleznyakova, Eliane Piket, Maria Needhamsen, Michael Hagemann-Jensen, Diana Ekman, Mohsen Khademi, Faiez Al Nimer, Patrick Scicluna, Omid R Faridani, Tomas Olsson, Fredrik Piehl, Maja Jagodic. Deposited on bioRxiv. https://www.biorxiv.org/content/10.1101/2020.05.15.097519v1 Profiling of small non-coding RNAs across cellular and biofluid compartments: implications for multiple sclerosis immunopathology. Galina Yurevna Zheleznyakova, Eliane Piket, Maria Needhamsen, Michael Hagemann-Jensen, Diana Ekman, Mohsen Khademi, Faiez Al Nimer, Patrick Scicluna, Omid R Faridani, Tomas Olsson, Fredrik Piehl, Maja Jagodic. Deposited on bioRxiv. https://www.biorxiv.org/content/10.1101/2020.05.15.097519v1 10.1101/2020.05.15.097519 2020 Zheleznyakova, G. Y., Piket, E., Needhamsen, M., Hagemann-Jensen, M., Ekman, D., Han, Y., James, T., Khademi, M., Al Nimer, F., Scicluna, P., Zheleznyakova, G., Piket, E., Needhamsen, M., Hagemann-Jensen, M., Ekman, D., Han, Y., James, T., Khademi, M., Al, N. F., … Jagodic, M. (2021). Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology. In PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (Vol. 118, Issue 17). https://doi.org/10.1073/pnas.2011574118 Zheleznyakova, G. Y., Piket, E., Needhamsen, M., Hagemann-Jensen, M., Ekman, D., Han, Y., James, T., Khademi, M., Al Nimer, F., Scicluna, P., Zheleznyakova, G., Piket, E., Needhamsen, M., Hagemann-Jensen, M., Ekman, D., Han, Y., James, T., Khademi, M., Al, N. F., … Jagodic, M. (2021). Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology. In PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (Vol. 118, Issue 17). https://doi.org/10.1073/pnas.2011574118 10.1073/pnas.2011574118 urn:nbn:se:su:diva-193708 oai:swepub.ki.se:462651 2021 oai:swepub.ki.se:462651