NBDC Research ID: hum0312.v2
SUMMARY
Aims: Genome-wide association studies (GWAS) have been conducted in multifactorial diseases such as autoimmune diseases, and more than 1000 disease susceptibility variants have been identified. However, GWAS only indicates the presence of disease-causing variants within a region. The effects of the accumulation of these variants on the functions of cells and tissues involved in disease states must be clarified. This study aims to integrate public GWAS data and expression quantitative trait loci (eQTL) and splicing QTL (sQTL) analyses to elucidate the pathogenesis of various multifactorial diseases through a comprehensive analysis of functional variants.
Methods:
[DRA016393 / DRA016394 / DDRA016395 / RA018714] Total RNAs from Lymphoblastoid Cell line (LCL) samples were used for Iso-seq and RNA-seq analyses
[DRA016285] Twenty-nine immune cell subsets were isolated from peripheral blood mononuclear cells using the 14-color cell sorter BD FACSAria Fusion. Total RNA was extracted, followed by polyA selection and cDNA library preparation using the SMART-seq v4 Ultra Low Input RNA Kit and SQK-LSK109 for cDNA library preparation. For flow cytometry staining panels, the definitions of the Human Immunology Project were followed. Neutrophils were recovered with EasySep Direct Human Neutrophil Isolation Kits or MACSxpress Neutrophil Isolation Kits human. The generated cDNA was sequenced by Flongle Flow Cell (long-read system).
Participants/Materials:
[DRA016393 / DRA016394 / DDRA016395 / RA018714] Samples with and without interferon (IFNa2) stimulation were obtained from LCL samples derived from the 1000 Genomes Registry.
[DRA016285] 29 immune cell types isolated from peripheral blood cells collected from a 42-year-old healthy individual
URL: https://www.tmd.ac.jp/english/press-release/20240528-3/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| NGS (Iso-seq) | Unrestricted-access | 2024/06/17 | |
| NGS (RNA-seq) | Unrestricted-access | 2024/06/17 | |
| DRA016285 | NGS (RNA-seq) | Unrestricted-access | 2024/06/20 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
2 healthy subjects DRA016394: 1 LCL sample with IFNa2 stimulation DRA018714: 2 LCL samples with and without IFNa2 stimulation (total 4 samples) |
| Targets | Iso-seq |
| Target Loci for Capture Methods | - |
| Platform | PacBio [Sequel II/IIe] |
| Library Source | Total RNA extracted from LCL samples |
| Cell Lines | GM19078, GM12878 (Coriell Institute) |
| Library Construction (kit name) | SMRTbell Express Template Prep Kit 3.0 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| DDBJ Sequence Read Archive ID | |
| Total Data Volume |
DRA016394: 4.6 GB (bam) DRA018714: 175.5 GB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
2 healthy subjects 4 LCL samples with and without IFNa2 stimulation (total 8 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Nanopore [MinION] |
| Library Source | Total RNA extracted from LCL samples |
| Cell Lines | GM19078, GM12878 (Coriell Institute) |
| Library Construction (kit name) | SMART-seq v4 Ultra Low Input RNA Kit |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| DDBJ Sequence Read Archive ID | DRA016393 |
| Total Data Volume | 335.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
94 healthy subjects 94 LCL samples with IFNa2 stimulation 20 LCL samples without IFNa2 stimulation |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | Total RNA extracted from LCL samples |
| Cell Lines | 94 samples (Coriell Institute) |
| Library Construction (kit name) | NEBNext UltraDirectional RNA Library Prep Kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| DDBJ Sequence Read Archive ID | DRA016395 |
| Total Data Volume | 335.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 1 healthy subject |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Nanopore [MinION] |
| Library Source | Total RNAs extracted from 29 immune cell subsets |
| Cell Lines | - |
| Library Construction (kit name) |
SMART-seq v4 Ultra Low Input RNA Kit SQK-LSK109 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| DDBJ Sequence Read Archive ID | DRA016285 |
| Total Data Volume | 335.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yuta Kochi
Affiliation: Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University
Project / Group Name: TRAnscriptomic resource of Immune cells using Long-read Sequencing (TRAILS)
URL: https://www.tmd.ac.jp/english/press-release/20240528-3/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Mechanisms of autoimmune disease pathogenesis through splicing QTLs in immune cells | 18H02849 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Investigating the physiological and pathological significance of NMD target transcripts through transomics analysis | 22H02597 |
| KAKENHI Grant-in-Aid for challenging Exploratory Research | Exploring the role of retroelements and their polymorphisms in autoimmune diseases | 21K19501 |
| KAKENHI Grant-in-Aid for JSPS Fellows | Elucidation of Sjögren's syndrome pathogenesis through retrotransposon sequences | 21J00596 |
| KAKENHI Grant-in-Aid for JSPS Fellows | Development of high-depth Isoformics techniques and creation of a spatiotemporal protein atlas | 21J15131 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Large-scale proteoform analysis for unveiling the entire view | 21H02459 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms | doi: 10.1038/s41467-024-48615-4 | DRA016285 |
| 2 |
