NBDC Research ID: hum0416.v3

 

SUMMARY

Aims: In order to grasp the biological reactions and pathological conditions occurring in the body in more detail for diseases involving immune reactions, blood and tissue samples were used and analyzed by following the changes and changes over time for each patient. The present research will acquire and profile comprehensive parameters for each patient and explore factors related to disease conditions and treatments. Then, it will be linked to the understanding of pathology and the development of therapeutic methods through the confirmation of changes in the found molecules and the search for functions.

Methods: single-cell CITE-seq (Cellular indexing of transcriptomes and epitopes), BD Ab-seq

Participants/Materials: microscopic polyangiitis (MPA), systemic sclerosis (SSc), healthy donors

 

Dataset IDType of DataCriteriaRelease Date
E-GEAD-635 NGS (CITE-seq) Unrestricted-access 2023/08/10
DRA019233 NGS (BD Ab-seq) Unrestricted-access 2024/09/27
E-GEAD-867 NGS (BD Ab-seq) Unrestricted-access 2024/09/27
DRA019274 NGS (CITE-seq, BD Ab-seq) Unrestricted-access 2024/10/16
E-GEAD-872 NGS (CITE-seq, BD Ab-seq) Unrestricted-access 2024/10/16

*Release Note

*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

CITE-seq

Participants/Materials

[E-GEAD-635]

microscopic polyangiitis (ICD10: M31.7): 8 cases

    blood samples were collected from 3 patients twice and 5 patients once

7 healthy donors

[DRA019274 / E-GEAD-872]

systemic sclerosis (ICD10: M34): 21 cases

    blood samples were collected from a patient three times and 20 patients once

6 healthy donors (3 are also used in E-GEAD-635)

Targets CITE-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500, NovaSeq 6000]
Library Source RNAs extracted from a single cell isolated from PBMCs
Cell Lines -
Library Construction (kit name) Chromium Single Cell 5' Reagent Kits v2
Fragmentation Methods Enzymatic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 91 bp
Software CellRanger (version 6.0.6)
Reference Genome Sequence GRCh38
QC Methods Cell Ranger Metrics
DDBJ Sequence Read Archive ID DRA019274
Genomic Expression Archive ID

E-GEAD-635

E-GEAD-872

Total Data Volume

E-GEAD-635: 311 MB (expression matrix, HDF5)

DRA019274: 1.83 TB (fastq)

E-GEAD-872: 800 MB (expression matrix, HDF5)

Comments (Policies) NBDC policy

 

BD Ab-seq

Participants/Materials

[DRA019233 / E-GEAD-867]

microscopic polyangiitis (ICD10: M31.7): 6 cases (4 cases are also used in E-GEAD-635)

7 healthy donors (5 are also used in E-GEAD-635, 2 are also used in DRA019274 / E-GEAD-872)

[DRA019274 / E-GEAD-872]

SSc (ICD10: M34) with renal crisis: 1 case

Targets BD Ab-seq
Target Loci for Capture Methods Information on the antibodies used for antibody sequencing
Platform Illumina [HiSeq 2500, NovaSeq 6000]
Library Source

[DRA019233 / E-GEAD-867]

RNAs extracted from a single cell isolated from white blood cells

[DRA019274 / E-GEAD-872]

RNAs extracted from a single cell isolated from whole blood leukocytes and kidney biopsy specimens

Cell Lines -
Library Construction (kit name) BD Rhapsody WTA Reagent Kit
Fragmentation Methods Enzymatic Fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Software BD Rhapsody Sequence Analysis Pipeline (version 1.12)
Reference Genome Sequence GRCh38
QC Methods Cell Ranger Metrics
DDBJ Sequence Read Archive ID

DRA019233

DRA019274

Genomic Expression Archive ID

E-GEAD-867

E-GEAD-872

Total Data Volume

DRA019233: 2 TB (fastq)

E-GEAD-867: 10 GB (expression matrix, txt)

DRA019274: 218 GB (fastq)

E-GEAD-872: 800 MB (expression matrix, txt)

Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Takehisa Kitazawa

Affiliation: Research Division, Chugai Pharmaceutical Co., Ltd.

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number

 

PUBLICATIONS

TitleDOIDataset ID
1 Single-cell multi-omics analysis identifies two distinct phenotypes of newly-onset microscopic polyangiitis doi: 10.1038/s41467-023-41328-0 E-GEAD-635
2 Neutrophil single-cell analysis identifies a uniquely primed subset and provides insights into predicting relapse of autoimmune small vessel vasculitis E-GEAD-867
3 Single-cell analysis reveals immune cell abnormalities underlying the clinical heterogeneity of systemic sclerosis DRA019274
E-GEAD-872