HCC-090-03-1H
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 HCC-090-03-1H, generated 2026-07-09 12:54:49 +0800.
804Cells analyzed
10Clusters
20,868Expressed genes
11660Mean UMI
2462Mean genes
6.964Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 10 | 0.7836 | 2.248 | 8 |
| Proliferation | 10 | 0.5366 | 1.7318 | 7 |
| Myeloid_APC | 10 | 0.4753 | 2.2949 | 9 |
| Epithelial_tumor | 10 | 0.4559 | 1.0018 | 5 |
| Endothelial | 10 | 0.1335 | 0.5466 | 7 |
| T_NK_cytotoxic | 10 | 0.0968 | 0.7372 | 10 |
| Checkpoint_exhaustion | 10 | 0.0495 | 0.1868 | 8 |
| Fibroblast_stroma | 10 | 0.0224 | 0.1323 | 8 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 176 | 11630.1989 | 2819.5 | 8.1637 |
| cluster_2 | 127 | 12951.5748 | 2963 | 8.5685 |
| cluster_3 | 126 | 10342.0794 | 995.5 | 2.6999 |
| cluster_4 | 92 | 7365.9457 | 1121.5 | 4.2774 |
| cluster_5 | 81 | 16865.6914 | 3587 | 8.4802 |
| cluster_6 | 59 | 7552.6102 | 2070 | 8.0354 |
| cluster_7 | 51 | 13239.3725 | 3456 | 8.1221 |
| cluster_8 | 42 | 18591.9524 | 4102.5 | 8.7383 |
| cluster_9 | 26 | 6010.8077 | 1750.5 | 7.2274 |
| cluster_10 | 24 | 11451.0417 | 2985.5 | 8.7514 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_3 | 1 | IGHG1 | 5.2331 | 6.717 | 1 |
| cluster_4 | 1 | IGHG1 | 4.8358 | 6.5865 | 0.9891 |
| cluster_1 | 1 | HLA-DRA | 3.8824 | 4.7919 | 1 |
| cluster_6 | 1 | HLA-DRA | 3.0714 | 4.6054 | 0.9661 |
| cluster_5 | 1 | APOA2 | 2.604 | 5.9424 | 1 |
| cluster_8 | 1 | APOA2 | 2.5054 | 5.9753 | 1 |
| cluster_2 | 1 | FGB | 2.4762 | 4.4873 | 1 |
| cluster_10 | 1 | HIST1H1C | 2.153 | 2.876 | 1 |
| cluster_9 | 1 | CCL5 | 1.9575 | 2.1113 | 0.7692 |
| cluster_7 | 1 | IFI27 | 1.8604 | 2.924 | 1 |
| cluster_3 | 2 | IGHG4 | 4.86 | 6.8627 | 1 |
| cluster_4 | 2 | IGHG4 | 4.8266 | 7.0386 | 1 |
| cluster_1 | 2 | RNASE1 | 3.8774 | 4.0564 | 0.9602 |
| cluster_6 | 2 | HLA-DRB1 | 2.6999 | 4.0688 | 0.9661 |
| cluster_2 | 2 | FGG | 2.4579 | 4.5579 | 1 |
| cluster_5 | 2 | ALB | 2.383 | 6.6204 | 1 |
| cluster_8 | 2 | STMN1 | 2.226 | 3.1104 | 1 |
| cluster_10 | 2 | FGG | 1.9007 | 4.3322 | 1 |
| cluster_9 | 2 | CD69 | 1.8545 | 1.9405 | 0.8077 |
| cluster_7 | 2 | IFITM3 | 1.7151 | 4.046 | 1 |
| cluster_3 | 3 | IGLC2 | 4.2074 | 5.1596 | 0.8651 |
| cluster_1 | 3 | C1QB | 3.7528 | 3.9801 | 1 |
| cluster_4 | 3 | IGHG3 | 2.8587 | 3.9811 | 0.9783 |
| cluster_6 | 3 | CD74 | 2.5899 | 4.8794 | 0.9831 |
| cluster_5 | 3 | SERPINA1 | 2.369 | 5.7975 | 1 |
| cluster_2 | 3 | APOC3 | 2.3676 | 4.8206 | 1 |
| cluster_8 | 3 | AMBP | 2.1178 | 4.7461 | 1 |
| cluster_10 | 3 | FGB | 1.8182 | 4.1661 | 1 |
| cluster_9 | 3 | CD52 | 1.7668 | 2.1549 | 0.8077 |
| cluster_7 | 3 | TM4SF1 | 1.5266 | 1.7115 | 0.9216 |
| cluster_1 | 4 | HLA-DRB1 | 3.573 | 4.3579 | 1 |
| cluster_3 | 4 | IGHG3 | 3.4684 | 4.3744 | 0.9524 |
| cluster_4 | 4 | MZB1 | 2.6304 | 3.2477 | 0.9891 |
| cluster_6 | 4 | HLA-DPB1 | 2.5064 | 3.4897 | 1 |
| cluster_2 | 4 | ALB | 2.3462 | 6.4531 | 1 |
| cluster_5 | 4 | AMBP | 2.2872 | 4.7957 | 1 |
| cluster_8 | 4 | HIST1H4C | 2.083 | 3.5518 | 1 |
| cluster_10 | 4 | H1F0 | 1.7986 | 2.6179 | 1 |
| cluster_9 | 4 | TRBC2 | 1.7152 | 1.7342 | 0.9615 |
| cluster_7 | 4 | IFITM2 | 1.462 | 2.7881 | 1 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-090-03-1H
Sample ID
HCC-090-03-1H
Dataset
CancerSCEM 2.0
Cohort
CancerSCEM 2.0 Chinese subset; Hepatocellular Cancer
Age / Age Group
Pan-cancer Chinese cohort, per-donor ages not in CancerSCEM metadata
Sex
Not reported in public CancerSCEM metadata
Health Status
Hepatocellular Cancer; Tumour
Tissue / Cell Source
Tumour
Modality
scRNA-seq (GEXSCOPE)
Cell Count
804
Analysis Status
Matrix available; UMAP generated
UMAP Status
Ready
Metadata / Source Notes
Project ID: HCC-090; Cancer type: Hepatocellular Cancer; Source: NCBI (GEO); Accession: GSE242889; Country: CHN; Sample type: Tumour; Protocol: GEXSCOPE; Matrix: HCC-090-03-1H.counts.matrix.tsv.gz (2.50 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=804; raw genes=23497; Leiden clusters=10; coordinates TSV and summary JSON are available online.; 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
Hepatocellular Cancer
cancer type short
HCC
library count
1
library sample ids
HCC-090-03-1H
source reference
CancerSCEM 2.0 metadata table; data source=NCBI (GEO); accession=GSE242889; downloaded 2026-07-06
data accession
GSE242889
project id
HCC-090
sample type
Tumour
country
CHN
data source
NCBI (GEO)
accession no
GSE242889
construction protocol
GEXSCOPE
transcriptome profile
Yes
metabolic profile
Yes
matrix status
Matrix available
matrix file name
HCC-090-03-1H.counts.matrix.tsv.gz
matrix file size bytes
2619117
matrix file size mb
2.50
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=804; raw_genes=23497; leiden_clusters=10; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated