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Data Archives

*Note: In this section, "GeMDBJ archives" means that the files were previously available from "the GeMDBJ database", which was discontinued and has been succeeded by this database. For a further information on the previous GeMDBJ database, please refer to "GeMDBJ Document Archives" below (the files are in Japanese).

JSNP Genome Scan (GeMDBJ archives)

Disease ReadMe SNP Frequency Data
5 Disease Combined (1st screening) html JGS1st_5diseases_combined.zip
Alzheimer's disease (1st screening) html JGS1st_AL.zip
Gastric cancer (1st screening) html JGS1st_GC.zip
Diabetes mellitus (1st screening) html JGS1st_ML.zip
Hypertension (1st screening) html JGS1st_HT.zip
Bronchial asthma (1st screening) html JGS1st_ZN.zip
Alzheimer's disease (2nd screening) html JGS2nd_AL.zip
Gastric cancer (2nd screening) html JGS2nd_GC.zip
Diabetes mellitus (2nd screening) html JGS2nd_ML.zip
Hypertension (2nd screening) html JGS2nd_HT.zip
Bronchial asthma (2nd screening) html JGS2nd_ZN.zip

Description SNP/Gene symbollist
5 Disease Combined (1st screening) JGS1st_5diseases_combined_without_freq.zip

Description ID list
Correspondence table of JSNP ID and dbSNPrs ID JSNP_dbSNPrs.zip

Illumina 110K Genome Scan (GeMDBJ archives)

Disease SNP Frequency Data
All group combined 110K-combined.zip
Japanese population control (female) 110K-japanese_ctl_female.zip
Japanese population control (male) 110K-japanese_ctl_male.zip
Patients with various types of cancers 110K-various_cancers.zip

Pharmacogenomic analyses ReadMe SNP Data
Pharmacokinetic parameters of gemcitabine (AUC) html GEM_GWAS_PKSNP_AUC.zip
Pharmacokinetic parameters of gemcitabine (Kel) html GEM_GWAS_PKSNP_Kel.zip
Pharmacokinetic parameters of gemcitabine (Volume) html GEM_GWAS_PKSNP_V.zip
Pharmacokinetic parameters of gemcitabine (Cmax) html GEM_GWAS_PKSNP_Cmax.zip
Pharmacokinetic parameters of gemcitabine (MRT) html GEM_GWAS_PKSNP_MRT.zip

Illumina 550K/610K Genome Scan (GeMDBJ archives)

Disease SNP Frequency Data
Japanese population control Tokyo 550K_610K_control_tokyo.zip
Osaka 550K_610K_control_osaka.zip
Ibaraki 550K_610K_control_ibaraki.zip
Tokyo+Osaka+Ibaraki 550K_610K_control_3_areas_combined.zip
Alzheimer's disease 550K_610K_AL.zip
Pancreatic cancer 550K_610K_PC.zip
Bronchial asthma 550K_610K_BA.zip

SNP Data

Accession ID Data
GWAS030 GC_Set.xlsx
GWAS031 datafile1.xls
SubmissionDataTemplate_v2_Revised.xls

Candidate Gene Approach (GeMDBJ archives)

Project ID Description SNP/Gene symbol
list
Frequency
data
CGA01 Allele frequencies of single nucleotide polymorphisms (SNPs) in 40 candidate genes for gene-environment studies on cancer: data from population-based Japanese random samples. zip -
CGA02 Polymorphisms in cancer-related genes. zip zip
CGA03 Polymorphisms in genes coding for Drug-Responsive Molecules. zip -
CGA04 Case-control study on 198 patients with pancreatic cancer and 182 controls. zip zip
CGA05 Allele frequencies of SNPs in the prion protein gene on Alzheimer's disease patients: data from population-based Japanese random samples. zip zip
CGA06 Genotype and allele frequencies of the TrkA gene SNPs in patients with sporadic Alzheimer's disease and control subjects zip zip
CGA07 Genotype and allele frequencies of the TrkA gene SNPs in patients with sporadic Alzheimer's disease and control subjects. zip zip
CGA08 Association between a missense polymorphism of the P75NTR gene and Alzheimer's disease, Association study between plasminogen activator urokinase gene and Alzheimer's disease, Association study between insulin-like growth factors (IGFs) and Alzheimer's disease. zip zip
CGA09 Allele frequencies of SNP in cystathionine-beta-synthase gene on senile dementia of Alzheimer type: data from population-based Japanese random samples. zip zip
CGA10 Allele frequencies of SNPs in ORMDL2 gene for gene-environment studies on Alzheimer's disease: data from population-based Japanese random samples. zip -
CGA11 Allele frequencies of SNPs in UCH-L1 gene for gene-environment studies on Alzheimer's disease: data from population-based Japanese random samples and patients of Alzheimer's disease. zip zip
CGA12 Genotype and allele frequencies of 5,438 SNPs in 222 candidate genes coding for drug metabolizing enzymes or transporters analyzed by RIKEN: data on 1,518 Japanese people including cancer patients and healthy volunteers. zip zip
CGA13 A case-control study on 570 patients with breast cancer and 497 controls in Thailand. zip zip

JPHC Study (a genome cohort in Japan)

Description .vcf file
Whole exome sequencing using Agilent SureSelect Human All Exon V4+UTRs+lincRNAotal was performed on germline DNA of the total 192 participants of JPHC Study from different regions in Japan (17 from Iwate, 15 from Akita, 35 from Ibaraki, 13 from Niigata, 19 from Nagano, 21 from Kochi, 28 from Nagasaki, 10 from Okinawa (Chubu) and 34 from Okinawa (Miyako)). In addition, whole genome sequencing was performed on 28 participants from Ibaraki. The non-reference allele call results, including false positives, were aggregated in a VCF file of the Japanese people with average health conditions, so that the file can be used as a Panel Of Normal samples (PON, see below).

About PON
MuTect, which is a method developed at the Broad Institute, identifies somatic point mutations in next generation sequencing data of cancer genomes. MuTect can use a Panel Of Normal samples (PON) filter to screen out variant calls, which are likely false positive. This VCF file was assembled as one of the standard PONs of Japanese people and is ready for the use by the MuTect pipeline. The file has the aggregated information of the non-reference allele calls by MuTect and includes false positive results.
GenomeCohort.hg19.muTect1.PON.zip

:PON by bwa (aln) mapping to hg19 and called by MuTect

GenomeCohort.hg19.MuTect2.PON.zip

:PON by bwa (mem) mapping to hg19 and called by MuTect2

Whole exome sequencing using Agilent SureSelect Human All Exon V4+UTRs+lincRNAotal was performed on germline DNA of the total 192 participants of JPHC Study from different regions in Japan (17 from Iwate, 15 from Akita, 35 from Ibaraki, 13 from Niigata, 19 from Nagano, 21 from Kochi, 28 from Nagasaki, 10 from Okinawa (Chubu) and 34 from Okinawa (Miyako)). In addition, whole genome sequencing was performed on 28 participants from Ibaraki. The VCF files in the right box contain the aggregated information of the non-reference allele calls by UnifiedGenotyper/HaplotypeCaller and include filtered results. GenomeCohort.hg19.MUG.zip

:MUG by bwa (aln) mapping to hg19 and called by UnifiedGenotyper

GenomeCohort.hg19.MHC.zip

:MHC by bwa (mem) mapping to hg19 and called by HaplotypeCaller


Expression Analysis (GeMDBJ archives)

Experiment ID Experiment Name GeMDBJ format MAGE-ML format .cel file(s)
EXPR001 Normal tissue series. zip zip zip*
EXPR002 Kidney (Non-cancerous, Adenocarcinoma) zip zip zip*
EXPR003 Kidney (Cell line) zip zip zip*
EXPR004 Stomach (Cell line) zip zip zip*
EXPR005 Blood, Leukocyte (Normal, Acute myeloid leukemia) zip zip zip*
EXPR006 Blood, Cells Panel (Asthma) zip zip zip*
EXPR007 Blood, PBMC (LPS/CpG stimulation time course) zip zip zip*
EXPR008 Blood vessel, Cell line, Umbilical vein endothelial cell, HUVEC zip zip zip*
EXPR009 Brain, Brain cortex (Amyotrophic lateral sclerosis as control , Alzheimer's disease) zip zip zip*
EXPR010 Blood, PBMC (LPS stimulation time course) zip zip zip*
EXPR011 Stomach (Cell line/spontaneous, 5Aza-dC+TSA) zip zip zip*
zip*
zip*
zip*
EXPR012 Stomach (Non-cancerous, Cancerous) zip zip zip*
EXPR013 B cell (Control vs. Teatment) zip zip zip*
EXPR014 Eosinophil (Control vs. Teatment) zip zip zip*
EXPR015 NK cell (Spontaneous) zip zip zip*
EXPR016 CBMC (Spontaneous) zip zip zip*
EXPR017 CBMC (Spontaneous) zip zip zip*
EXPR018 PBMC zip zip zip*
EXPR019 PBMC (Control vs. Teatment) zip zip zip*
EXPR020 PBMC (Control vs. Teatment) zip zip zip*
EXPR021 PBMC (Control vs. Teatment) zip zip zip*
EXPR022 PBMC (Control vs. Teatment) zip zip zip*
EXPR023 PBMC (Control vs. Teatment) zip zip zip*
EXPR024 PBMC (Control vs. Teatment) zip zip zip*
EXPR025 PBMC (Control vs. Teatment) zip zip zip*
EXPR026 PBMC (Control vs. Teatment) zip zip zip*
EXPR027 PBMC (GeneChip protocol comparison) zip zip zip*
EXPR028 PBMC (Spontaneous) zip zip zip*
EXPR029 RPMI8226 (Control vs. Teatment) zip zip zip*
EXPR030 RPMI8226 (Control vs. Teatment) zip zip zip*
EXPR031 THP-1 (Control vs. Teatment) zip zip zip*
EXPR032 Whole Blood (RNA extraction protocol comparison) zip zip zip*
EXPR033 Whole Blood (Spontaneous) zip zip zip*
EXPR034 A549 (Control vs. Teatment) zip zip zip*
EXPR035 A549 (Control vs. Teatment) zip zip zip*
EXPR036 A549 (Control vs. Teatment) zip zip zip*
EXPR037 BEAS-2B (Control vs. Teatment) zip zip zip*
EXPR038 BEAS-2B (Teatment) zip zip zip*
EXPR039 NHBE (Control vs. Teatment) zip zip zip*
EXPR040 NHBE (Spontaneous) zip zip zip*
EXPR041 NHEK-Neo (Control vs. Teatment) zip zip zip*
EXPR042 Reference Total RNA (GeneChip protocol comparison) zip zip zip*
EXPR043 Lung, (Non-cancerous, NSCLC:non-small-cell lung cancer) zip zip zip*
zip*
zip*
zip*
zip*
EXPR044 Liver, (Non-cancerous, Nodule-in-nodule type HCC early and progressed components) zip zip zip*
EXPR045 Liver, (Non-cancerous, HCCs with and without intrahepatic metastasis) zip zip zip*
EXPR046 Head and Neck (carcinoma) zip zip zip*
EXPR047 Esophagus (Non-cancerous/Neoplasm) zip zip zip*
zip*
zip*
zip*
zip*
zip*
zip*
EXPR048 Esophagus (Neoplasm) zip zip zip*
EXPR050 Liver (Cell line) zip zip zip*
EXPR051 Pancreas (Cell line) zip zip zip*
EXPR052 Ovary (Cell line) zip zip zip*
EXPR053 Pancreas (Xenografts of primary tumors) zip zip zip*
EXPR054P Soft tissue (Pleomorphic malignant fibrous histiocytoma, Myxofibrosarcoma) zip zip zip*
EXPR055P EPCs, HUVEC, LMEC, AoEC (using PCR amplified cDNA) zip zip zip*
EXPR056 Pancreatic carcinoma (Cell line) zip zip zip*
EXPR058P Soft tissue (Pleomorphic malignant fibrous histiocytoma, Myxofibrosarcoma, Myxoid liposarcoma, Synovial sarcoma, Leiomyosarcoma, Fibrosarcoma, and Malignant peripheral nerve sheath tumor) zip zip ---

*Zip files will be about three times larger after the decompression. Please check your free space of HDD.


mRNA Array

Accession ID Data
EXPR059 EXPR059.zip

Proteome (GeMDBJ archives)

Project Name Description Expression Analysis Protein Information
Pancreatic cancer cell line 9 cancer cell lines and 2 normal cell lines. zip zip
Esophageal cancer 53 tumor tissues and 58 normal epithelial tissues. zip zip
Ewing's sarcoma 3 cases with good prognosis and 5 cases with poor prognosis zip zip
Lung Adenocarcinoma 262 tumor tissues from patients with resected stage IA-IIIA lung adenocarcinoma. zip zip
Malignant Pleural Mesothelioma 11 malignant pleural mesothelioma tissues, 11 lung adenocarcinoma tissues, 13 lung squamous cell carcinoma tissues, 3 pleomorphic carcinoma tissues, and 6 synovial sarcoma tissues zip zip
Colorectal cancer 66 colorectal cancer tissues and 67 normal colon mucosal tissues. zip zip
Cholangiocarcinoma 10 cancer cell lines, 9 xenograft tissues and 13 primary tumor tissues. zip zip
Liver cancer cell line 21 cancer cell lines. zip zip

DIGE QuickViewer Installer, Manual (Japanese Only)
zip

GeMDBJ Documents (only in Japanese, GeMDBJ archives)

Description Document
GeMDBJ The GeMDBJ leaflet in Japanese GeMDBJ_leaflet-j.pdf
The GeMDBJ first step guide in Japanese GeMDBJ-1st-step-guide-j.pps
The GeMDBJ manual in Japanese GeMDBJ-manual-j.pdf
JSNP Genome Scan (JGS) Population stratification analyses on the 1st screening data of the JSNP genome scan (in Japanese) JGS-1st-stage-stratif-rpt.pdf
Illumina 550K/610K Genome Scan (550K/610K) The report of in-silico quality control of the genome scan data by "Sentrix HumanHap550 Genotyping BeadChip" and "InfiniumHD 610-Quad" (Illumina) (in Japanese) DryQCreport550K610K.pdf
The report of association analysis using the haplotype and diplotype (in Japanese) Haplotype.pdf
The report of GWAS data analysis of Alzheimer's disease (in Japanese) AlzheimersReport.pdf
The report of GWAS data analysis of asthma (in Japanese) AsthmaReport.pdf
The report of GWAS data analysis of diabetes (in Japanese) DiabetesReport.pdf
The report of GWAS data analysis of pancreatic cancer (in Japanese) PancreasReport.pdf
JPHC Study (a genome cohort in Japan) Comparison of GATK pipelines (in Japanese) GenomeCohortWEScompChr9and21.pdf
Comparison of GATK pipelines for the wholle-genome and whole-exome sequencing (in Japanese) GenomeCohortWGSandWES.pdf