NBDC Research ID: hum0345.v1
SUMMARY
Aims: To clarify the differentiation pathway and mechanism of human lymphoid and dendritic cells from hematopoietic stem cells
Methods: CD34+ cells or target cells in CD34+ cells were sorted and assessed for scRNA-seq and ATAC-seq analyses. Obtained findings were evaluated by culture on a co-culture system.
Participants/Materials:
Cord blood (30-50ml) was obtained from healthy volunteers and kept in a freezer after the selection of CD34+ cells. Mixtures of several samples were used for experiments.
- One mixed sample (CD34+) of 2 volunteers' cord blood
- One mixed sample (CD10SP) of 30 volunteers' cord blood
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000528 JGAS000551 |
Controlled-access (Type I) | 2022/08/05 |
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MOLECULAR DATA
| Participants/Materials: | 30 healthy volunteers (ATAC-seq were also performed for 1. samples) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source |
RNAs extracted from CD34+ cells or lymphoid fractions from mixed cord blood of healthy volunteers 1. CD34+ cells from 2 volunteers' cord blood 2. CD10SP fraction from 30 volunteers' cord blood |
| Cell Lines | - |
| Library Construction (kit name) |
1. Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (10x Genomics) 2. 10X Genomics Chromium |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
1. 118 bp 2. 300-500 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
1. JGAD000647 2. JGAD000671 |
| Total Data Volume |
1. 76.6 GB (fastq) 2. 41.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | 2 healthy volunteers |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from CD34+ cells from 2 healthy volunteers' cord blood |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (10x Genomics) |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 99 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000647 |
| Total Data Volume | 76.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Kohshi Ohishi
Affiliation: Transfusion Medicine and Cell Therapy, Mie University Hospital
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Study of human lymphopoiesis and neoplastic transformation with novel culture system | 18K08322 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Science | 16H06279 |
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 |
|---|---|---|---|---|---|
