Small non-coding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology
SND-ID: snd1150-1. Version: 1.0. DOI: https://doi.org/10.5878/c1mq-9r62
Download all files
Citation
Creator/Principal investigator(s)
Galina Zheleznyakova - Karolinska Institutet, Department of Clinical Neuroscience
Eliane Piket - Karolinska Institutet, Department of Clinical Neuroscience
Maria Needhamsen - Karolinska Institutet, Department of Clinical Neuroscience
Maja Jagodic - Karolinska Institutet, Department of Clinical Neuroscience
Research principal
Karolinska Institutet
- Department of Clinical Neuroscience
Description
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 cel
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. Show less..
Data contains personal data
No
Language
Unit of analysis
Population
Multiple Sclerosis patients (29), non-inflammatory neurological disease patients (11), Systemic lupus erythematosus patients (5)
Study design
Observational study
Description of study design
Small non-coding RNAs were isolated from PBMC, plasma, CSF cells and CSF. The libraries were prepared as previously described (PMID: 27798564) and sequenced on two lanes of HiSeq2500. The data analysis was performed as previously described (PMID: 27798564).
Sampling procedure
Biobank is connected to the study
Yes
Variables
4
Number of individuals/objects
176
Geographic spread
Geographic location: Sweden, Stockholm County, Stockholm Municipality
Responsible department/unit
Department of Clinical Neuroscience
Contributor(s)
Mohsen Khademi - Karolinska Institutet, Department of Clinical Neuroscience
Diana Ekman - National Bioinformatics Infrastructure Sweden
Tomas Olsson - Karolinska Institutet, Department of Clinical Neuroscience
Faiez Al Nimer - Karolinska Institutet, Department of Clinical Neuroscience
Patrick Scicluna - Karolinska Institutet, Department of Clinical Neuroscience
... Show more..Mohsen Khademi - Karolinska Institutet, Department of Clinical Neuroscience
Diana Ekman - National Bioinformatics Infrastructure Sweden
Tomas Olsson - Karolinska Institutet, Department of Clinical Neuroscience
Faiez Al Nimer - Karolinska Institutet, Department of Clinical Neuroscience
Patrick Scicluna - Karolinska Institutet, Department of Clinical Neuroscience
Omid Faridani - Karolinska Institutet, Ludwig Institute for Cancer Research
Michael Hagemann-Jensen - Karolinska Institutet, Ludwig Institute for Cancer Research
Fredrik Piehl - Karolinska Institutet, Department of Clinical Neuroscience
Show less..Ethics Review
Stockholm - Ref. 2009/2107-31/2
Research area
Medical and health sciences (Standard för svensk indelning av forskningsämnen 2011)
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
DOI:
https://doi.org/10.1101/2020.05.15.097519
If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.
