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/

Data Set ID	Type of Data	Criteria	Release Date
JGAS000253	NGS (RNA-seq, CAGE-seq)	Controlled Access (Type I)	2020/11/20

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

MOLECULAR DATA

RNA-seq


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 https://www.chubu-cbb.org
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 Data set ID	JGAD000356
Total Data Volume	152 GB (fastq, bed [ref: GRCh38])
Comments (Policies)	NBDC policy

CAGE-seq


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 Data set 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	Data Set ID
1	Maximal Therapeutic Vulnerability Converges on XIAP and BCL2 1 in Aggressive Acute Myeloid Leukemia with Diverse Genetic Aberrations		JGAD000356
2

USRES (Controlled-Access Data)

Principal Investigator:	Affiliation:	Data in Use (Data Set ID)	Period of Data Use