10.5878/c1mq-9r62
Zheleznyakova, Galina
Galina
Zheleznyakova
Department of Clinical Neuroscience, Karolinska Institutet
Piket, Eliane
Eliane
Piket
Department of Clinical Neuroscience, Karolinska Institutet
Needhamsen, Maria
Maria
Needhamsen
Department of Clinical Neuroscience, Karolinska Institutet
Jagodic, Maja
Maja
Jagodic
Department of Clinical Neuroscience, Karolinska Institutet
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
Karolinska Institutet
2021
Multiple Sclerosis
Multipel skleros
Multiple Sclerosis, Relapsing-Remitting
Remitterande multipel skleros
Demyelinating Autoimmune Diseases, CNS
Demyeliniserande autoimmuna sjukdomar, CNS
Demyelinating Diseases
Demyeliniserande sjukdomar
Autoimmune Diseases of the Nervous System
Autoimmuna nervsjukdomar
Leukoencephalopathies
Leukoencefalopatier
Nervous System Diseases
Nervsystemets sjukdomar
Brain Diseases
Hjärnsjukdomar
Autoimmune Diseases
Autoimmuna sjukdomar
Central Nervous System Diseases
Centrala nervsystemets sjukdomar
Immune System Diseases
Immunsjukdomar
small non-coding RNA analysis
small non-coding RNA analysis
Multiple Sclerosis, Secondary-Progressive
sekundär progressiv multipel skleros
Medical and Health Sciences
Medicin och hälsovetenskap
Olsson, Tomas
Tomas
Olsson
Department of Clinical Neuroscience, Karolinska Institutet
Al Nimer, Faiez
Faiez
Al Nimer
Department of Clinical Neuroscience, Karolinska Institutet
Scicluna, Patrick
Patrick
Scicluna
Department of Clinical Neuroscience, Karolinska Institutet
Faridani, Omid
Omid
Faridani
Ludwig Institute for Cancer Research, Karolinska Institutet
Hagemann-Jensen, Michael
Michael
Hagemann-Jensen
Ludwig Institute for Cancer Research, Karolinska Institutet
Piehl, Fredrik
Fredrik
Piehl
Department of Clinical Neuroscience, Karolinska Institutet
Khademi, Mohsen
Mohsen
Khademi
Department of Clinical Neuroscience, Karolinska Institutet
Ekman, Diana
Diana
Ekman
National Bioinformatics Infrastructure Sweden
2021-04-08
eng
10.5878/hp5f-3b39
10.1101/2020.05.15.097519
214.34 MiB
4 variables
176 cases
1.0
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
Stockholm County
Stockholm Municipality
Swedish Association of persons with Neurological disabilities
Horizon 2020
Swedish Research Council
Swedish MS Foundation
Swedish Society for Medical Research
AstraZeneca-Science for Life Laboratory collaboration
Stockholm County Council
Swedish Brain Foundation