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 IDType of DataCriteriaRelease Date
JGAS000617 NGS (RNA-seq) Controlled-access (Type I) 2023/08/29
E-GEAD-623 NGS (RNA-seq) Unrestricted-access 2023/08/29

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

*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

JGAS000617 / E-GEAD-623

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use