NBDC Research ID: hum0406.v1
SUMMARY
Aims: The ideal way of studying the disease is to use an affected part (tissue) of the patient's body. However, the use of the affected tissue involves many issues; for example, sampling of the affected tissue may impose a severe burden on the patient or is sometimes technically impossible. Therefore, iPS cells are a powerful technology that can differentiate into the various tissues that make up our bodies. The aim of this study is to generate iPS cells from patients’ and/or their family members’ somatic cells and to use them together with clinical information to discover more about the cause of the diseases and to develop new effective treatments.
Methods: Patient iPSC-derived type 2 alveolar epithelial (iAT2) cells (EpCAM+CPM+) and fibroblasts (EpCAM-CPM-) were isolated by fluorescence-activated cell sorting. Total RNA was extracted from the cells and sequenced.
Participants/Materials:
- EpCAM+CPM+ or EpCAM-CPM- cells of alveolar organoids derived from iPSCs established from PBMCs of a familial interstitial pneumonia patient with Y104H variant of SFTPC
- EpCAM+CPM+ or EpCAM-CPM- cells of Y104H-KO iPSC-derived alveolar organoids established from PBMCs of the patient with Y104H variant of SFTPC
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000617 | NGS (RNA-seq) | Controlled-access (Type I) | 2023/08/29 |
| E-GEAD-623 | NGS (RNA-seq) | Unrestricted-access | 2023/08/29 |
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*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
| Participants/Materials |
Familial interstitial pneumonia with SFTPC variant (ICD10: J84.9): 1 case - EpCAM+CPM+ or EpCAM-CPM- cells of alveolar organoids derived from iPSCs established from PBMCs of the patient with Y104H variant of SFTPC: 3 samples each - EpCAM+CPM+ or EpCAM-CPM- cells of Y104H-KO iPSC-derived alveolar organoids established from PBMCs of the patient with Y104H variant of SFTPC: 3 samples each |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 2000] |
| Source | RNAs extracted from EpCAM+CPM+ or EpCAM-CPM- cells derived from iPSCs established from PBMCs of a patient with Y104H variant of SFTPC |
| Cell Lines | - |
| Library Construction (kit name) | Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit |
| Fragmentation Methods | Exposure to divalent cations at elevated temperatures |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 59 bp x 2 |
| Mapping Methods | STAR 2.7.10b |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | HTSeq package |
| QC Methods | RSeQC package |
| Gene Number | 36,602 genes |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000746 |
| Genomic Expression Archive ID | E-GEAD-623 |
| Total Data Volume |
JGAD000746: 27.7 GB (fastq) E-GEAD-623: 2.16 MB (csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shimpei Gotoh
Affiliation: Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED) | Application of human iPS cells for disclosing the pathogenic mechanisms of intractable respiratory diseases and finding novel therapeutic agents | JP17bm0804007 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Cryptotanshinone is a candidate therapeutic agent for interstitial lung disease associated with a BRICHOS-domain mutation of SFTPC | doi: 10.1016/j.isci.2023.107731 | JGAD000746 E-GEAD-623 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
