BRCA-128-01-1A
De-identified Human Immune Atlas donor/sample detail for CancerSCEM 2.0. The record preserves available public metadata while avoiding direct identifiers.
Donor-Level Analysis Results
Matrix-backed CancerSCEM donor analysis for BRCA-128-01-1A, generated 2026-07-09 12:54:49 +0800.
1,998Cells analyzed
10Clusters
17,549Expressed genes
1078Mean genes
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 10 | 0.2799 | 0.8075 | 6 |
| T_NK_cytotoxic | 10 | 0.105 | 0.2076 | 9 |
| Myeloid_APC | 10 | 0.0742 | 0.291 | 9 |
| Checkpoint_exhaustion | 10 | 0.0653 | 0.0916 | 8 |
| Proliferation | 10 | 0.0242 | 0.0448 | 3 |
| Endothelial | 10 | 0.0152 | 0.0768 | 4 |
| Fibroblast_stroma | 10 | 0.0141 | 0.0786 | 7 |
| Epithelial_tumor | 10 | 0.0026 | 0.007 | 6 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 268 | 904.5 | ||
| cluster_10 | 263 | 1258 | ||
| cluster_5 | 249 | 1261 | ||
| cluster_7 | 237 | 1056 | ||
| cluster_9 | 233 | 1164 | ||
| cluster_4 | 217 | 690 | ||
| cluster_3 | 184 | 1099 | ||
| cluster_2 | 162 | 818.5 | ||
| cluster_8 | 104 | 1203.5 | ||
| cluster_6 | 81 | 1119 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_8 | 1 | HLA-DRA | 2.1404 | 2.4339 | 0.9712 |
| cluster_3 | 1 | BANK1 | 1.879 | 2.111 | 0.9783 |
| cluster_6 | 1 | BANK1 | 1.7849 | 2.1176 | 0.963 |
| cluster_5 | 1 | CMSS1 | 1.3198 | 1.8505 | 0.8153 |
| cluster_9 | 1 | BACH2 | 1.2937 | 3.126 | 0.9914 |
| cluster_10 | 1 | ANXA1 | 1.2879 | 1.6446 | 0.8593 |
| cluster_7 | 1 | FOS | 1.1344 | 2.1739 | 0.9536 |
| cluster_4 | 1 | JUN | 0.4941 | 1.3113 | 0.7051 |
| cluster_1 | 1 | LINC00861 | 0.4513 | 0.5896 | 0.5709 |
| cluster_2 | 1 | IKZF1 | 0.3535 | 1.0237 | 0.8148 |
| cluster_8 | 2 | CD83 | 1.9906 | 2.2246 | 1 |
| cluster_3 | 2 | AFF3 | 1.8483 | 2.1842 | 0.9728 |
| cluster_6 | 2 | RALGPS2 | 1.5113 | 1.8611 | 0.9753 |
| cluster_10 | 2 | FTH1 | 1.2754 | 2.485 | 0.9544 |
| cluster_5 | 2 | BACH2 | 1.2509 | 3.0781 | 0.988 |
| cluster_7 | 2 | JUN | 1.0959 | 1.8368 | 0.8945 |
| cluster_9 | 2 | FYN | 1.0526 | 2.2241 | 0.9742 |
| cluster_1 | 2 | INPP4B | 0.4467 | 1.0109 | 0.7463 |
| cluster_4 | 2 | HSPA1A | 0.388 | 0.4773 | 0.3318 |
| cluster_2 | 2 | THEMIS | 0.3041 | 0.7488 | 0.5864 |
| cluster_8 | 3 | SIPA1L1 | 1.8726 | 2.3842 | 0.9808 |
| cluster_3 | 3 | CD74 | 1.5545 | 1.9943 | 0.9783 |
| cluster_6 | 3 | CD74 | 1.2862 | 1.817 | 0.9506 |
| cluster_5 | 3 | PDE3B | 1.1567 | 2.1079 | 0.9398 |
| cluster_10 | 3 | SIK3 | 1.1178 | 2.5555 | 1 |
| cluster_7 | 3 | TNFAIP3 | 1.0908 | 2.0252 | 0.9241 |
| cluster_9 | 3 | PLCL1 | 0.9486 | 1.7078 | 0.8455 |
| cluster_1 | 3 | RIPOR2 | 0.4132 | 1.2675 | 0.8433 |
| cluster_4 | 3 | IGFBP7 | 0.3632 | 0.3942 | 0.2673 |
| cluster_2 | 3 | BCL11B | 0.2671 | 0.9917 | 0.7778 |
| cluster_8 | 4 | CD74 | 1.8422 | 2.3293 | 0.9904 |
| cluster_3 | 4 | MEF2C | 1.5273 | 1.6951 | 0.9185 |
| cluster_6 | 4 | ARHGAP24 | 1.2173 | 1.3117 | 0.8765 |
| cluster_5 | 4 | FILIP1L | 1.1222 | 1.5435 | 0.7631 |
| cluster_10 | 4 | LINC01619 | 1.0469 | 2.0156 | 0.962 |
| cluster_7 | 4 | CD69 | 0.999 | 1.8403 | 0.9536 |
| cluster_9 | 4 | RGCC | 0.9171 | 1.5536 | 0.8798 |
| cluster_1 | 4 | BCL11B | 0.4029 | 1.0951 | 0.8806 |
| cluster_4 | 4 | LDB2 | 0.3593 | 0.3715 | 0.2442 |
| cluster_2 | 4 | MAML2 | 0.2625 | 1.3486 | 0.8889 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
BRCA-128-01-1A
Sample ID
BRCA-128-01-1A
Dataset
CancerSCEM 2.0
Cohort
CancerSCEM 2.0 Chinese subset; Breast Cancer
Age / Age Group
Pan-cancer Chinese cohort, per-donor ages not in CancerSCEM metadata
Sex
Not reported in public CancerSCEM metadata
Health Status
Breast Cancer; Tumour
Tissue / Cell Source
Tumour
Modality
scRNA-seq (10X Genomics)
Cell Count
10,452
Analysis Status
Matrix available; UMAP generated by fallback sampled pipeline
UMAP Status
Ready
Metadata / Source Notes
Project ID: BRCA-128; Cancer type: Breast Cancer; Source: NCBI (GEO); Accession: GSE225600; Country: CHN; Sample type: Tumour; Protocol: 10X Genomics; Matrix: BRCA-128-01-1A.counts.matrix.tsv.gz (13.87 MB); Matrix integrity: gzip file ended before end-of-stream marker during UMAP generation; redownload required before UMAP can be generated.; Age/sex not reported in public CancerSCEM metadata. Age source: CancerSCEM 2.0 database; 400 samples across 47 cancer types; donor-level age not included in download.csv
Additional Clinical / Source Fields
Supplementary source metadata retained from the migrated manifest where available.
cancer type
Breast Cancer
cancer type short
BRCA
library count
1
library sample ids
BRCA-128-01-1A
source reference
CancerSCEM 2.0 metadata table; data source=NCBI (GEO); accession=GSE225600; downloaded 2026-07-06
data accession
GSE225600
project id
BRCA-128
sample type
Tumour
country
CHN
data source
NCBI (GEO)
accession no
GSE225600
construction protocol
10X Genomics
transcriptome profile
Yes
metabolic profile
Yes
matrix status
Matrix incomplete; redownload required
matrix file name
BRCA-128-01-1A.counts.matrix.tsv.gz
matrix file size bytes
14548737
matrix file size mb
13.87
umap coordinates url
umap summary url
umap pipeline
Fallback Python normalize_total/log1p/HVG/SVD/UMAP; sampled 3000/10452 cells; generated 2026-07-09
matrix integrity status
Gzip EOF/truncated during UMAP generation