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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000899

Type of data
NGS (WGS, RNA-seq, EM-seq, t-nanoEM)
Access criteria
Controlled-access (Type I)
Total data volume
774 GB
File formats
  • FASTQ
Research
hum0200
Date published
2024-11-26
Date modified
2024-11-26
DDBJ Search
JGAD000899 (opens in a new tab)
JGA Study
JGAS000758 (opens in a new tab)

Analysis method

WGS

Materials and participants
IDC (ICD10: C509): 1 case
4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples*, non-tumor tissues: 2 samples*)
*exact same samples as EM-seq and t-nanoEM
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
DNAs extracted from tumor and non-tumor tissues
  • Tissue
    Breast
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
NEBNext Enzymatic Methyl-seq Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
300 bp
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
IDC (ICD10: C509): 1 case
4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples, non-tumor tissues: 2 samples)
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
RNAs extracted from tumor and non-tumor tissues
  • Tissue
    Breast
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
SMART-Seq Stranded Kit
Fragmentation
Heat treatment with Shearing Master Mix
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
300 bp
Data use policy
NBDC data sharing policy (JGAP000001)

EM-seq

Materials and participants
IDC (ICD10: C509): 1 case
4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples*, non-tumor tissues: 2 samples*)
*exact same samples as WGS (JGAS000758) and t-nanoEM
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
DNAs extracted from tumor and non-tumor tissues
  • Tissue
    Breast
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
EM-seq
Target
N/A
Reagent kit
NEBNext Enzymatic Methyl-seq Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
300 bp
Data use policy
NBDC data sharing policy (JGAP000001)

t-nanoEM (Nanopore methylation)

Materials and participants
IDC (ICD10: C509): 1 case
4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples*, non-tumor tissues: 2 samples*)
*exact same samples as WGS (JGAS000758) and EM-seq
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
DNAs extracted from tumor and non-tumor tissues
  • Tissue
    Breast
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
t-nanoEM
Target
Custom human methylome panel for long-read (Twist Bioscience, Order ID: MTE-9910638)
Reagent kit
NEBNext Enzymatic Methyl-seq Kit
Twist Standard Hyb and Wash Kit v2
Fragmentation
g-TUBE (Covaris)
Platform
Oxford Nanopore Technologies PromethION
Read type
Single-end
Read length
4400 bp (Mean)
Data use policy
NBDC data sharing policy (JGAP000001)