NBDC Research ID: hum0384.v1
SUMMARY
Aims: To identify genomic/epigenomic/transcriptomic features dysregulated in hematological malignancies through genomic/epigenetic/transcriptomic analyses of hematological malignant cells. Regarding identified epigenomic abnormalities, we perform further analysis to determine whether they could be good candidates to translate into therapy development. To this end, we will modulate the activity of targets by using their activators and inhibitors in vitro and establish xenograft mouse models of hematological malignancies and manipulate their activity in vivo. Through these studies, we develop new therapeutic agents or modalities that lead to improved patients’ prognoses.
Methods: A part of bone marrow aspirates (3 ml) obtained to perform a definite diagnosis will be provided for this study. Mononuclear cells are separated by gradient separation using Ficoll, then subjected to magnetic beads separation to purify CD34+ hematopoietic stem and progenitor cells (HSPCs). CD34+ HSPCs are subjected to RNA sequencing, target capture sequencing and ATAC sequencing analyses.
Participants/Materials: acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) specimens were collected at Komagome Hospital and its affiliated city hospitals. Normal cells were purchased from Lonza.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000603 | NGS (RNA-seq, Target Capture) | Controlled-access (Type I) | 2024/06/19 |
| JGAS000718 | NGS (RNA-seq, ATAC-seq) | Controlled-access (Type I) | 2024/06/19 |
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MOLECULAR DATA
| Participants/Materials |
[JGAS000603] AML (ICD10: C92.0): 4 cases MDS (ICD10: D46): 30 cases healthy control: 4 samples [JGAS000718] healthy control: 2 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500/2500] |
| Library Source | RNAs extracted from tumor cells and normal cells |
| Cell Lines | LONZA 2M-101A, 2M-101C: Bone Marrow CD34+ cells |
| Library Construction (kit name) | SMARTer Ultra Low Input RNA Kit for Sequencing, NEBNext Ultra DNA Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 60 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000732: 79.6 GB (fastq) JGAD000851: 179.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
AML (ICD10: C92.0): 4 cases MDS (ICD10: D46): 30 cases |
| Targets | Target Capture |
| Target Loci for Capture Methods | QIAseq DHS-003Z: Human Myeloid Neoplasms Panel |
| Platform | Illumina [MiSeq] |
| Library Source | DNAs extracted from tumor cells |
| Cell Lines | - |
| Library Construction (kit name) | QIAseq Targeted DNA Panels |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000732 |
| Total Data Volume | 79.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
AML (ICD10: C92.0): 4 cases MDS (ICD10: D46): 30 cases healthy control: 6 samples |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500] |
| Library Source | DNAs extracted from tumor cells and normal cells |
| Cell Lines | LONZA 2M-101A, 2M-101C: Bone Marrow CD34+ cells |
| Library Construction (kit name) | NEBNext Ultra DNA Library Prep Kit |
| Fragmentation Methods | Tn5 transposase |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 60 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000851 |
| Total Data Volume | 179.5 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 (C) | Molecular basis of MDS pathogenesis and construction of novel MDS prognostic model | 21K08366 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
