NBDC Research ID: hum0399.v1
SUMMARY
Aims: To understand how metastasized breast cancer cells affect immune cells in lymph nodes
Methods: 10x Visium-based spatial transcriptome analyses
Participants/Materials: Two breast cancer patients harboring metastatic lymph nodes
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000616 | NGS (Visium Spatial Gene Expression), Histological image | Controlled-access (Type I) | 2024/06/12 |
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MOLECULAR DATA
| Participants/Materials |
Breast cancer (ICD10: C509) patients harboring metastatic lymph nodes: 2 cases non-metastatic lymph node: 2 samples metastatic lymph node: 2 samples |
| Targets | Visium Spatial Gene Expression, histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from lymph nodes |
| Cell Lines | - |
| Library Construction (kit name) | Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | |
| Software | Space Ranger v2.0.0 |
| Reference | GRCh38-2020-A |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000745 |
| Total Data Volume |
65.8 GB (fastq, png, json, csv, tiff, tsv, mtx, cloupe, html) |
| 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: Shinpei Kawaoka
Affiliation: Institute for Life and Medical Sciences, Kyoto University
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Sciences | 16H06279 |
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 |
|---|---|---|---|---|---|
