NBDC Research ID: hum0556.v1
SUMMARY
Aims: By analyzing thoracic tumor specimens and normal tissues, this study aims to elucidate the pathophysiology of cancer, thereby contributing to cancer prevention, the establishment of diagnostic and therapeutic methods, and the development of novel treatments.
Methods: ChIP-seq
Participants/Materials: Tumor samples from 17 patients with lung cancer
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000903 | NGS (ChIP-seq) | Controlled-access (Type I) | 2026/06/23 |
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MOLECULAR DATA
| Participants/Materials |
lung cancer (ICD10: C349): 17 cases tumor tissue: 24 samples (FFPE samples) |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNA extracted from tumor tissues was used for the library construction. Anti-histone antibody (H3K27ac) was used for immunoprecipitation. |
| Cell Lines | - |
| Library Construction (kit name) | ThruPLEX DNA-Seq Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Bioruptor) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 50 bp |
| QC |
- Read trimming using Trimmomatic (removal of TruSeq3 adapters; trimming when the average quality score across a 4-base sliding window falls below 20; removal of reads shorter than 36 bp) - Post-mapping filtering using Samtools (removal of reads with MAPQ < 20) |
| Mapping Methods | Bowtie2 |
| Reference Genome Sequence | hg19/GRCh37 |
| Detecting Methods for peaks | MACS2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001047 |
| Total Data Volume | 38 GB (fastq, bed) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takashi Sato
Affiliation: Department of Respiratory Medicine, Kitasato University School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Exploration of differentiation programs in lung cancers using epigenomic profiling | 20K17192 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Exploring the roles of master regulators in differentiation programs of various lung cancers | 23K07609 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Search for MYC-related biomarkers for lung neuroendocrine neoplasms | 22K08288 |
| MSD Life Science Foundation, Public Interest Incorporated Foundation | Heterogeneity and plasticity of differentiation programs in lung cancer | - |
| Medical Research Grant, Takeda Science Foundation | Deciphering the Heterogeneity and Plasticity of Differentiation Programs that Define Lung Cancer Phenotypes | - |
| The Naito Foundation | Investigating Plasticity in Lung Cancer Progression and Adaptation | - |
PUBLICATIONS
USRES (Controlled-access Data)
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Epigenomic profiling of neuroendocrine lung cancers identifies a classical-neuroendocrine ASCL1/NKX2-1 subtype and a SOX11-associated differentiation axis linked to reduced immunogenicity | doi: 10.1016/j.lungcan.2026.109464 | JGAD001047 |
| 2 |
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
