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/

 

Data Set IDType of DataCriteriaRelease Date
hum0056.v1.freq.v1 (1) Allele frequencies from WGS Un-restricted Access 2018/03/30
hum0056.v1.ch3.v1 (2) Methylation rates at each CpG site from WGBS Un-restricted Access 2018/03/30
hum0056.v1.fpkm.v1 (3) Average of FPKM values from RNA-seq Un-restricted Access 2018/03/30

*Release Note

*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

hum0056.v1.freq.v1

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 Data Set ID

hum0056.v1.freq.v1

(Click the Data Set ID to download the file)

Dictionary 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

 

hum0056.v1.ch3.v1

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 Data Set ID

hum0056.v1.ch3.v1

(Click the Data Set ID to download the file)

Dictionary 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

 

hum0056.v1.fpkm.v1

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 tempreture
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 Data Set ID

hum0056.v1.fpkm.v1

(Click the Data Set ID to download the file)

Dictionary 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):

NameTitleProject 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

TitleDOIData Set 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