HCC-090-04-1H
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-090-04-1H, generated 2026-07-09 12:54:49 +0800.
1,998Cells analyzed
21Clusters
21,918Expressed genes
8116Mean UMI
1912Mean genes
6.873Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 21 | 0.8079 | 2.8205 | 8 |
| Myeloid_APC | 21 | 0.7885 | 2.7146 | 9 |
| Endothelial | 21 | 0.4142 | 2.0837 | 7 |
| T_NK_cytotoxic | 21 | 0.3852 | 1.3399 | 10 |
| Proliferation | 21 | 0.3673 | 2.0539 | 7 |
| Fibroblast_stroma | 21 | 0.2235 | 1.8296 | 8 |
| Checkpoint_exhaustion | 21 | 0.097 | 0.3773 | 8 |
| Epithelial_tumor | 21 | 0.056 | 0.3584 | 5 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 265 | 9515.7245 | 1955 | 7.7874 |
| cluster_2 | 253 | 8399.3478 | 2327 | 6.8339 |
| cluster_3 | 217 | 6413.0415 | 2050 | 7.838 |
| cluster_4 | 178 | 17229.5449 | 1418 | 2.6534 |
| cluster_5 | 172 | 6137.1802 | 1746.5 | 7.6427 |
| cluster_6 | 146 | 4105.0411 | 1245 | 6.8556 |
| cluster_7 | 117 | 10678.0855 | 2713 | 5.2844 |
| cluster_8 | 110 | 7932.8364 | 1789 | 8.2138 |
| cluster_9 | 95 | 5869.2421 | 1534 | 7.8133 |
| cluster_10 | 81 | 6716.2716 | 1955 | 7.4929 |
| cluster_11 | 79 | 4425.6835 | 1325 | 7.3438 |
| cluster_12 | 61 | 6340.4754 | 1717 | 7.168 |
| cluster_13 | 56 | 4243.8036 | 1172 | 8.2466 |
| cluster_14 | 45 | 7641.3111 | 1918 | 6.4986 |
| cluster_15 | 36 | 4735.6944 | 1388 | 6.9146 |
| cluster_16 | 21 | 10028.0952 | 2158 | 4.4361 |
| cluster_17 | 19 | 4918.9474 | 1466 | 5.7628 |
| cluster_18 | 17 | 12152.6471 | 3385 | 6.6952 |
| cluster_19 | 14 | 8248.0714 | 1612.5 | 8.3589 |
| cluster_20 | 10 | 8199.8 | 1445 | 8.5024 |
| cluster_21 | 6 | 5902 | 1453 | 6.8763 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_4 | 1 | IGHG1 | 5.5446 | 6.2186 | 0.9831 |
| cluster_3 | 1 | ACTA2 | 4.3238 | 4.7284 | 1 |
| cluster_21 | 1 | ALB | 3.9128 | 5.5742 | 1 |
| cluster_7 | 1 | TM4SF1 | 3.7204 | 4.1521 | 0.9829 |
| cluster_9 | 1 | S100A9 | 3.6013 | 4.1133 | 0.9263 |
| cluster_16 | 1 | C1QB | 3.5435 | 4.2843 | 1 |
| cluster_19 | 1 | CST3 | 3.536 | 5.4727 | 1 |
| cluster_20 | 1 | BIRC3 | 3.4669 | 3.789 | 1 |
| cluster_1 | 1 | C1QB | 3.3972 | 3.7247 | 0.9358 |
| cluster_8 | 1 | HLA-DRA | 3.1649 | 4.9935 | 1 |
| cluster_14 | 1 | RGS5 | 3.1248 | 3.6855 | 0.9556 |
| cluster_10 | 1 | FCN3 | 3.0522 | 3.3504 | 0.9877 |
| cluster_17 | 1 | S100A9 | 2.898 | 3.5536 | 1 |
| cluster_2 | 1 | IGFBP7 | 2.6133 | 4.214 | 1 |
| cluster_18 | 1 | GNG11 | 2.5302 | 3.3535 | 1 |
| cluster_11 | 1 | CCL4 | 2.516 | 3.4462 | 0.9747 |
| cluster_12 | 1 | HMGB2 | 2.4338 | 3.2956 | 1 |
| cluster_5 | 1 | STMN1 | 2.2781 | 2.9957 | 1 |
| cluster_13 | 1 | MS4A1 | 1.9899 | 2.0445 | 0.9464 |
| cluster_6 | 1 | IL7R | 1.9214 | 2.5617 | 0.9726 |
| cluster_15 | 1 | TRBC2 | 1.6206 | 2.314 | 0.9722 |
| cluster_4 | 2 | IGHG3 | 5.3217 | 6.1797 | 0.9944 |
| cluster_3 | 2 | TAGLN | 4.0131 | 4.2732 | 1 |
| cluster_16 | 2 | C1QA | 3.4918 | 4.1016 | 1 |
| cluster_21 | 2 | SERPINA1 | 3.4119 | 4.7199 | 1 |
| cluster_7 | 2 | CLDN5 | 3.3814 | 3.6397 | 0.9915 |
| cluster_1 | 2 | FTL | 3.2419 | 6.4987 | 1 |
| cluster_9 | 2 | LYZ | 3.2375 | 4.1522 | 1 |
| cluster_19 | 2 | CD74 | 3.0525 | 5.6728 | 1 |
| cluster_14 | 2 | IGFBP7 | 2.9753 | 4.8399 | 1 |
| cluster_20 | 2 | RGS1 | 2.9716 | 4.4429 | 1 |
| cluster_8 | 2 | LYZ | 2.7965 | 3.7112 | 1 |
| cluster_10 | 2 | DNASE1L3 | 2.7271 | 3.3255 | 0.9877 |
| cluster_17 | 2 | S100A8 | 2.6999 | 3.1337 | 0.9474 |
| cluster_2 | 2 | AKAP12 | 2.6024 | 3.0415 | 0.9723 |
| cluster_18 | 2 | TUBA1B | 2.4016 | 3.692 | 1 |
| cluster_5 | 2 | HIST1H4C | 2.2753 | 2.8324 | 0.9186 |
| cluster_11 | 2 | CCL5 | 2.2649 | 3.2419 | 0.9241 |
| cluster_12 | 2 | TOP2A | 1.9984 | 2.1884 | 0.9836 |
| cluster_6 | 2 | CD52 | 1.7867 | 3.2425 | 0.9932 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-090-04-1H
Sample ID
HCC-090-04-1H
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
2,424
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-090-04-1H.counts.matrix.tsv.gz (5.85 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=2424; raw genes=22995; Leiden clusters=21; 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-090-04-1H
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-090-04-1H.counts.matrix.tsv.gz
matrix file size bytes
6129811
matrix file size mb
5.85
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=2424; raw_genes=22995; leiden_clusters=21; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated