NBDC Research ID: hum0243.v1
SUMMARY
Aims: Evaluation of function of immue cells using humanized mice
Methods: RNA-seq or CAGE-seq
Participants/Materials: RNAs extracted from cells derived from cord blood, and leukemia cells harvested from bone marrow aspirates or spleen cells of humanized mice generated from peripheral blood, bone marrow aspirates or samples from patients with Acute Myeloid Leukemia
URL： http://www.riken.jp/en/research/labs/ims/hum_dis_model/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000253 | NGS (RNA-seq, CAGE-seq) | Controlled-access (Type I) | 2020/11/20 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
Acute Myeloid Leukemia (ICD10: C920): 114 cases (166 samples) Cells derived from cord blood: 44 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from cells derived from cord blood, and leukemia cells harvested from bone marrow aspirates or spleen cells of humanized mice generated from peripheral blood, bone marrow aspirates or samples from patients with Acute Myeloid Leukemia |
| Cell Lines |
https://www.bs.jrc.or.jp/ktks/bbc/special/m6_03_00_index.html |
| Library Construction (kit name) | NEXT Ultra DNA Library Prep kit for Illumina |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 50 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000356 |
| Total Data Volume | 152 GB (fastq, bed [ref: GRCh38]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Acute Myeloid Leukemia (ICD10: C920): 27 cases (27 samples, 25 are also used in RNA-seq analysis) |
| Targets | CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from leukemia cells harvested from bone marrow aspirates or spleen cells of humanized mice generated from peripheral blood, bone marrow aspirates or samples from patients with Acute Myeloid Leukemia |
| Cell Lines | - |
| Library Construction (kit name) | Low Quantity single strand CAGE protocol *1 (See also: https://www.protocols.io/view/low-quantity-single-strand-cage-protocol-10bbwkipcw) |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 47 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000356 |
| Total Data Volume | 152 GB (fastq, bed [ref: GRCh38]) |
| Comments (Policies) | NBDC policy |
*1 M. S. Morioka et al., Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. Methods Mol Biol 2120, 277-301 (2020).
DATA PROVIDER
Principal Investigator: Fumihiko Ishikawa
Affiliation: Laboratory for Human Disease Models, Riken Center for Integrative Medical Sciences
Project / Group Name: Target AML project
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 2 | Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive Acute Myeloid Leukemia | doi: 10.1038/s43018-021-00177-w | JGAD000356 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Jinyan Huang | School of Medicine, Zhejiang University | Comprehensive analysis of alternative splicing in malignant tumors | JGAD000356 | 2022/03/07-2024/01/01 | |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000356 | 2022/12/26-2025/03/31 |
