hum0201-v2Release info

Collection and transfer of human tumor samples and research using genomic information / Transfer of existing samples and research using genomic information / Reseach of searching gene mutations in gastrointestinal chronic inflammatory diseases

Aims

Search for differences in genomics and traits among normal cells, digestive non-tumor cells (inflammatory cells), and tumor cells

Methods

JGAS000199: The organoids were established from epithelial tissues from patients, and cultured. DNAs were extracted from the organoids and peripheral blood cells. Whole exome sequencing analysis was performed to identify the somatic mutations.
JGAS000237: Organoids were established from tissue samples (normal and cancer) obtained from any cancer patients. The organoids were cultured, and DNA / RNA was extracted from the organoids for whole genome / RNA sequencing analysis to identify the somatic mutations. Blood samples were substituted when normal tissue samples were not available.
JGAS000256: RNA was extracted from the 2D-cultured normal duodenal organoids with or without medium rotation. RNA sequencing was performed to identify the changes in gene expression after culture medium rotation.
JGAS000378: RNA sequencing and Chip-seq analysis for the organoids derived from colon cancer tissues and a normal epithelial tissue from patients
JGAS000350: RNA sequencing analysis for the organoids derived from colon cancer tissues
JGAS000550: single cell RNA sequencing analysis for normal colonic tissue and RNA sequencing or Whole Exome sequencing analyses for the organoids derived from healthy normal colonic tissues in the neoplastic disease patient
JGAS000719: Organoids were derived from surgically resected specimens, endoscopic ultrasound-guided fine needle aspiration samples, brushing samples, pleural effusion, and ascites of patients with pancreatic cancer. Genetically engineered human pancreatic duct organoids were made by introducing cancer gene mutations in duct organoids using CRISPR-Cas9. DNAs/RNAs were extracted from the organoids for whole exome sequencing, RNA sequencing, single cell RNA sequencing, ATAC sequencing, and ChIP sequencing analyses.
JGAS000881: Organoids were established from the tumor and normal counterpart of patients with duodenal tumor. Also, organoids were established from healthy ileum, colon or duodenum of patients with colon cancer, stomach cancer or a healthy individual and were further genetically engineered with CRISPR-Cas9. DNAs/RNAs were extracted from the organoids for whole exome sequencing and RNA sequencing analyses.

Participants/materials

JGAS000199: Controls who underwent colonoscopy, gastrointestinal inflammatory disease patients, and neoplastic disease patients
JGAS000237: Neoplastic disease patients
JGAS000256: Normal duodenum tissue from a neoplastic disease patient
JGAS000378: Colon cancer tissues and a normal epithelial tissue from neoplastic disease patients
JGAS000350: Neoplastic disease patient
JGAS000550: Neoplastic disease patient
JGAS000719: Pancreatic cancer patients
JGAS000881: Colon cancer patients, duodenal adenoma patients, a stomach cancer patient and a healthy individual

URL

N/A

Principal investigator

Toshiro Sato

Affiliation

Department of Organoid Medicine, Keio University School of Medicine

No research projects.