NBDC Research ID: hum0464.v1
SUMMARY
Aims: Radical treatments for hematopoietic tumors such as leukemia, myelodysplastic syndromes, myeloproliferative tumors, and multiple myeloma have not been fully established. One of the major factors hindering the efforts to find such treatments is the difficulty in constructing model mice that appropriately mimic the disease state. In this study, we collected peripheral blood or bone marrow cells from patients with hematological tumors and attempted in vitro cultures and molecular cell biological analyses, including genetic and epigenetic studies. Based on the knowledge gained from these studies, we aim to create patient-derived xenograft mouse models of hematological tumors and further develop new therapeutic approaches.
Methods: A part of bone marrow aspirates obtained to establish a definite diagnosis or evaluate the disease status was provided for this study. Mononuclear cells were separated by gradient separation using Ficoll, and then subjected to magnetic beads separation or FACS sorting to purify tumor cells. Next, they were subjected to RNA sequencing to analyze gene expression profiles.
Participants/Materials:
[RNA-seq] A total of 86 bone marrow samples from 17 multiple myelomas
[single-cell RNA-seq, scBCR-seq] A total of 22 bone marrow samples from 9 multiple myelomas
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000723 | NGS (RNA-seq, scRNA-seq, scBCR-seq) | Controlled-access (Type I) | 2024/07/25 |
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MOLECULAR DATA
| Participants/Materials |
multiple myeloma (ICD10: C90.0): 17 cases bone marrow: 86 samples 11 fractions: 8 cases (60 samples) CD138 positive/negative cell pairs: 13 cases (26 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000, NextSeq 2000] |
| Library Source | RNAs extracted from 11 fractions of cells or CD138+/- cells |
| Cell Lines | - |
| Library Construction (kit name) | SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, SMART-Seq HT Kit, NEBNext Ultra DNA Library Prep Kit for Illumina |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 70 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000856 |
| Total Data Volume | 143.0 GB（fastq） |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
multiple myeloma (ICD10: C90.0): 9 cases bone marrow: 22 samples (scRNA-seq: 11 samples, scBCR-seq: 11 samples) |
| Targets | scRNA-seq, scBCR-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | RNAs extracted from CD38+ cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit v2, Chromium Single Cell Human BCR Amplification Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 90 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000856 |
| Total Data Volume | 143.0 GB（fastq） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Atsushi Iwama
Affiliation: Division of Stem Cell and Molecular Medicine Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (S) | Pathogenec implication of hematopoietic stem cell aging in age-associated hematological malignancies | JP24H00066 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
