NBDC Research ID: hum0215.v1
SUMMARY
Aims: Application to future medicine by analyzing Alzheimer's disease-associated genes
Methods: Whole RNA-seq of blood cells
Participants/Materials: Alzheimer's disease, mild cognitive impairment, and healthy individuals
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000532 | Transcripts Per Kilobase Million (TPM) data calculated from NGS (RNA-seq) | Controlled-access (Type I) | 2022/09/28 |
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MOLECULAR DATA
| Participants/Materials |
Alzheimer's disease (ICD10: F00): 317 cases Mild cognitive impairment (ICD10: F06.7): 432 cases Healthy controls: 107 individuals |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded Total RNA with Ribo-Zero Globin and IDT for Illumina TruSeq UD Indexes |
| Fragmentation Methods | Enzymatic fragmentation (Elute, Prime, Fragment High Mix) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Mapping Methods | STAR (ver. 2.5.2b) |
| Reference Genome Sequence | GRCh37 |
| Detecting method for read count (software) | subread package (ver. 1.6.6) |
| QC | FastQC (ver. 0.11.7) and Cutadapt (ver. 1.16) |
| Gene Number | about 50,000 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000651 |
| Total Data Volume | 48 MB (csv [TPM data]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kouichi Ozaki
Affiliation: Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Health, Labour and Welfare Sciences Research Grants for Research on Dementia | Integrative analysis for omics and clinical data to facilitate the precision medicine for dementia. | |
| Research Funding for Longevity Sciences from the NCGG | Genomic and transcriptome analysis for geriatric diseases. | 21-23 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through immune landscape analysis | doi: 10.1038/s41514-022-00096-9 | JGAD000651 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
