NBDC Research ID: hum0069.v1

 

SUMMARY

Aims: MicroRNAs (miRNAs), particularly those found in human body fluids, have been suggested as potential biomarkers. Among various body fluids, the cerebrospinal fluid (CSF) shows promise as a profiling target for diagnosis and monitoring of neurological diseases. However, relevant genome-scale studies are limited and no studies have profiled exosomal miRNAs in CSF. Therefore, we conducted a next-generation sequencing-based survey of small RNAs in the exosomal and non-exosomal (supernatant) fractions of healthy human CSF as well as serum in each donor. Our data provided the first landscape of small RNAs in CSF exosome.

Methods: Samples were derived from three donors and subjected to a NGS-based survey. CSF samples were obtained via lumbar puncture, centrifuged to remove contaminating cells. Corresponding serum samples were simultaneously isolated from peripheral blood. Samples were further divided into exosomal and supernatant fractions via ultracentrifugation. Total RNA was isolated from each individual fractionated sample (Qiagen). Small RNA libraries were prepared using a TruSeq Small RNA Library Prep Kit (Illumina). Individual libraries were prepared with unique indexes, pooled and subjected to 50-base reads in single lanes of a HiSeq 2500 system (Illumina). Small RNA sequences were aligned to the human reference genome (hg19) using BWA (version 0.5.9). Small RNA clusters were annotated as miRNAs when their genomic coordinates overlapped with those of miRNAs registered in miRbase (version 20). The number of reads aligned within each individual cluster was normalized to counts per million (CPM) after applying a normalization factor based on the relative log expression method via edgeR. Post-processed reads were also analysed using the script ‘quantifier.pl’ in the miRdeep2 package (version 2.0.0.7; based on the miRbase database).

Participants/Materials: CSF and serum samples from three donors (neuromuscular disease patients) were analyzed.

URL: http://www.tmd.ac.jp/med/nuro/study2-e.html

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000064 NGS (small RNA-seq) Controlled Access (Type I) 2016/12/09

*Release Note 

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MOLECULAR DATA

JGAS00000000064

Participants/Materials

Neuromuscular disease (control group) : 3 patients

(6 pairs of CSF and serum samples, total 12 samples)

Targets small RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source Total RNA extracted from exosome of CSF and serum samples from three donors
Cell Lines -
Library Construction (kit name) TruSeq Small RNA Library Prep Kit (Illumina)
Fragmentation Methods -
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 50 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000064
Total Data Volume

5 GB

  Data files : 12 (fastq)

  Analysis files : 1 (other [ref: hg19])

Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Takanori Yokota

Affiliation: Tokyo Medical and Dental University, Department of Neurology and Neurological Science

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
Project Focused on Developing Key Technology for Discovering and Manufacturing Drugs for Next-Generation Treatment and Diagnosis, Japan Agency for Medical Research and Development (AMED) / New Energy and Industrial Technology Development Organization (NEDO) Development of Diagnostic Technology for Detection of miRNA in Body Fluids 16ae0101016h00039

 

PUBLICATIONS

TitleDOIData Set ID
1 Next-generation sequencing-based small RNA profiling of cerebrospinal fluid exosomes. doi: 10.1016/j.neulet.2016.10.042 JGAD00000000064
2

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Ana M. Aransay CIC bioGUNE JGAD00000000064 2018/12/18-2019/01/31