NBDC Research ID: hum0056.v1
SUMMARY
Aims: To provide genome and multi-layer omics data from a population based cohort (Iwate Medical Megabank: IMM) to research communities
Methods: Allele frequencies based on whole genome sequencing (WGS), methylation rates based on whole genome bisulfite sequencing (WGBS), and FPKM values based on RNA sequencing (RNA-seq) of 102 monocytes, 102 CD4+ T cells, and 94 neutrophils (total 197 individuals from IMM cohort) isolated from peripheral blood cells.
Participants/Materials: Monocytes and CD4+ T cells from 102 individuals, and neutrophils from 94 individuals in each (total 197 individuals)
URL: http://imethyl.iwate-megabank.org/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0056.v1.freq.v1 | (1) Allele frequencies from WGS | Unrestricted-access | 2018/03/30 |
| hum0056.v1.ch3.v1 | (2) Methylation rates at each CpG site from WGBS | Unrestricted-access | 2018/03/30 |
| hum0056.v1.fpkm.v1 | (3) Average of FPKM values from RNA-seq | Unrestricted-access | 2018/03/30 |
*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 | IMM cohort: 197 individuals |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500/HiSeq X] |
| Library Source | DNAs extracted from 102 monocytes, 102 CD4+ T cells, and 94 neutrophils |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free HT Sample Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris LE220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 162 bp (72 neutrophils: 150 bp) |
| QC | qMiSeq*1 |
| Deduplication | none |
| Calibration for re-alignment and base quality | none |
| Mapping Methods | Bowtie2 (version 2.1.0) |
| Reference Genome Sequence | GRCh37d5 |
| Coverage (Depth) | 40.9 × |
| Detecting Methods for Variation | Bcftools software (ver. 0.1.17-dev) |
| Total Reads / Uniquely Mapped Reads |
230,956,735,490 / 228,318,012,630 (Monocytes: 58,859,522,366 / 57,737,359,722) (CD4+ T cells: 58,964,563,094 / 57,845,976,317) (neutrophils: 113,132,650,030 / 112,734,676,591) *mapped reads: a read which had multiple mapped locations was aligned to one site randomly. |
| Filtering Methods | minor allele count (MAC) > 1 |
| SNP Numbers (after QC) |
Monocytes: 8,129,415 SNPs CD4+ T cells: 8,137,443 SNPs Neutrophils: 8,175,808 SNPs |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume |
Monocytes: 403 MB (txt) CD4+ T cells: 403.5 MB (txt) neutrophils: 409 MB (txt) |
| Comments (Policies) | NBDC policy |
*1: Katsuoka et al, Analytical Biochemistry, 2014
| Participants/Materials | IMM cohort : 197 individuals |
| Targets | WGBS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from 102 monocytes, 102 CD4+ T cells, and 94 neutrophils |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA Methylation Kit |
| Fragmentation Methods | bisulfite conversion reaction |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| QC | electrophoresis and qPCR |
| Deduplication | SAMtools (ver.0.1.19) |
| Calibration of re-alignment and base quality | none |
| Mapping Methods | NovoAlign (ver.3.02.08) |
| Reference Genome Sequence | GRCh37d5 |
| Coverage (Depth) |
Monocytes: 31.1 ± 1.6 CD4+T cells: 31.0 ± 1.6 Neutrophils: 54.7 ± 1.6 |
| Detecting Methods for Variation | NovoMethyl (ver.3.02.08) |
| Total Reads / Uniquely Mapped Reads |
Monocytes: 780,709,034 ± 45,934,514 / 624,432,868 ± 38,766,158 CD4+ T cells: 779,212,752 ± 40,833,955 / 667,934,331 ± 33,002,407 Neutrophils: 1,144,935,054 ± 33,512,764 / 994,992,101 ± 32,667,070 |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume |
Monocytes: 1.4 GB (txt) CD4+ T cells: 1.4 GB (txt) neutrophils: 1.5 GB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | IMM cohort : 197 individuals |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from 102 monocytes, 102 CD4+ T cells, and 94 neutrophils |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Library Preparation Kit v2 |
| Fragmentation Methods | divalent cation under high temperature |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| QC | electrophoresis and qPCR |
| Deduplication | none |
| Calibration of re-alignment and base quality | none |
| Mapping Methods | TopHat (ver. 2.0.13) |
| Reference Genome Sequence | GRCh37, Human GENCODE Gene Set (release 19) |
| Coverage (Depth) | - |
| Detecting Methods for Variation | cuffquant and cuffnorm |
| Total Reads / Uniquely Mapped Reads |
Monocytes: 33,917,157 ± 3,153,528 / 27,390,039 ± 2,494,286 CD4+ T cells: 35,175,996 ± 1,275,575 / 27,506,624 ± 1,669,459 Neutrophils: 47,040,140 ± 6,289,540 / 43,241,139 ± 8,491,065 |
| Gene Numbers |
Monocytes: 16,282 genes CD4+ T cells: 18,299 genes Neutrophils: 14,534 genes |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume |
Monocytes: 818 KB (txt) CD4+ T cells: 919 KB (txt) neutrophils: 731 KB |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Atsushi Shimizu
Affiliation: Disaster Reconstruction Center, Iwate Medical University
Project / Group Name: Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Ministry of Education, Culture, Sports, Science and Technology Japan | Tohoku Medical Megabank Project | |
| Japan Agency for Medical Research and Development (AMED) | Tohoku Medical Megabank Project (Iwate Medical University) Special Account of the Great East Japan Earthquake Disaster Recovery | JP18km0105003 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies | doi: 10.1038/s41525-017-0016-5 |
