HCC-090-08-1H
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-090-08-1H, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
18Clusters
21,149Expressed genes
5132Mean UMI
1402Mean genes
6.892Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| Myeloid_APC | 18 | 0.648 | 2.2858 | 9 |
| B_plasma | 18 | 0.629 | 2.372 | 8 |
| T_NK_cytotoxic | 18 | 0.4905 | 1.311 | 10 |
| Proliferation | 18 | 0.1591 | 1.5962 | 7 |
| Endothelial | 18 | 0.0989 | 0.9562 | 7 |
| Checkpoint_exhaustion | 18 | 0.0872 | 0.2295 | 8 |
| Epithelial_tumor | 18 | 0.0824 | 1.0811 | 7 |
| Fibroblast_stroma | 18 | 0.0177 | 0.1401 | 8 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 390 | 3313.0359 | 1077 | 6.8489 |
| cluster_2 | 230 | 3534.9957 | 1228 | 7.5199 |
| cluster_3 | 172 | 3353.8895 | 1118.5 | 6.6525 |
| cluster_4 | 166 | 6579.1807 | 1788 | 6.2571 |
| cluster_5 | 165 | 12227.3333 | 1079 | 3.3117 |
| cluster_6 | 157 | 6765.7834 | 1767 | 8.17 |
| cluster_7 | 131 | 3460.7023 | 1177 | 8.1445 |
| cluster_8 | 104 | 4728.3654 | 1646.5 | 7.3464 |
| cluster_9 | 101 | 3504.198 | 1146 | 7.3245 |
| cluster_10 | 96 | 6843 | 1915 | 7.4923 |
| cluster_11 | 84 | 3732.9167 | 1213 | 5.9002 |
| cluster_12 | 68 | 6389.1176 | 1601.5 | 8.2276 |
| cluster_13 | 40 | 7455 | 1778.5 | 7.804 |
| cluster_14 | 38 | 4226.5 | 1177 | 7.4132 |
| cluster_15 | 26 | 3745.7308 | 1119.5 | 8.9308 |
| cluster_16 | 18 | 4885.2222 | 1858 | 8.0886 |
| cluster_18 | 7 | 4440.7143 | 1455 | 6.0423 |
| cluster_17 | 7 | 4313 | 740 | 1.809 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_17 | 1 | ALB | 6.1232 | 6.444 | 1 |
| cluster_14 | 1 | TPSB2 | 5.415 | 5.4676 | 1 |
| cluster_5 | 1 | IGHG4 | 4.7679 | 5.3926 | 0.9333 |
| cluster_4 | 1 | C1QB | 3.8092 | 4.0624 | 1 |
| cluster_12 | 1 | S100A9 | 3.7022 | 4.2062 | 0.9559 |
| cluster_6 | 1 | HLA-DRA | 3.1783 | 4.3762 | 1 |
| cluster_18 | 1 | ALB | 2.9382 | 3.2702 | 1 |
| cluster_13 | 1 | CST3 | 2.7956 | 4.0744 | 0.9 |
| cluster_10 | 1 | STMN1 | 2.7537 | 2.9563 | 1 |
| cluster_11 | 1 | S100A9 | 2.7478 | 3.2623 | 1 |
| cluster_16 | 1 | TM4SF4 | 2.6731 | 2.7349 | 1 |
| cluster_8 | 1 | IGFBP7 | 2.4841 | 2.6149 | 0.9135 |
| cluster_15 | 1 | MS4A1 | 2.094 | 2.1508 | 0.9615 |
| cluster_9 | 1 | CCL5 | 2.0301 | 3.9355 | 1 |
| cluster_7 | 1 | GNLY | 1.7332 | 2.0278 | 0.855 |
| cluster_2 | 1 | CCL4 | 1.6926 | 3.5008 | 0.9957 |
| cluster_3 | 1 | IL7R | 1.4728 | 2.1361 | 0.9709 |
| cluster_1 | 1 | IL7R | 1.137 | 1.7053 | 0.8872 |
| cluster_17 | 2 | APOA2 | 5.5548 | 5.6497 | 1 |
| cluster_5 | 2 | IGHG1 | 4.7152 | 5.1226 | 0.903 |
| cluster_14 | 2 | TPSAB1 | 4.3206 | 4.3325 | 1 |
| cluster_4 | 2 | C1QA | 3.7395 | 3.9529 | 1 |
| cluster_12 | 2 | LYZ | 3.6362 | 4.1945 | 1 |
| cluster_6 | 2 | CST3 | 3.0466 | 4.1421 | 1 |
| cluster_10 | 2 | HIST1H4C | 2.7453 | 3.1952 | 0.9271 |
| cluster_13 | 2 | CD74 | 2.6243 | 4.6775 | 1 |
| cluster_16 | 2 | ANXA4 | 2.5402 | 2.6437 | 1 |
| cluster_11 | 2 | S100A8 | 2.3862 | 2.8015 | 0.9762 |
| cluster_8 | 2 | IFI27 | 2.1826 | 2.4503 | 0.9423 |
| cluster_18 | 2 | APOA1 | 2.1218 | 2.1851 | 1 |
| cluster_7 | 2 | NKG7 | 1.5608 | 2.6646 | 0.9924 |
| cluster_15 | 2 | HLA-DRA | 1.5414 | 2.9687 | 1 |
| cluster_2 | 2 | NKG7 | 1.4939 | 2.5281 | 0.9957 |
| cluster_3 | 2 | KLRB1 | 1.3497 | 2.183 | 0.9535 |
| cluster_9 | 2 | CD52 | 1.0177 | 2.6611 | 0.9703 |
| cluster_1 | 2 | CCL5 | 0.9718 | 2.7902 | 0.9154 |
| cluster_17 | 3 | TTR | 5.2089 | 5.2791 | 1 |
| cluster_5 | 3 | IGKC | 4.4287 | 5.4505 | 0.9818 |
| cluster_14 | 3 | CPA3 | 4.1062 | 4.1281 | 1 |
| cluster_4 | 3 | C1QC | 3.4437 | 3.6327 | 1 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-090-08-1H
Sample ID
HCC-090-08-1H
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; Normal
Tissue / Cell Source
Normal
Modality
scRNA-seq (GEXSCOPE)
Cell Count
2,718
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: Normal; Protocol: GEXSCOPE; Matrix: HCC-090-08-1H.counts.matrix.tsv.gz (5.11 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=2718; raw genes=22447; Leiden clusters=18; 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-090-08-1H
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
Normal
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-090-08-1H.counts.matrix.tsv.gz
matrix file size bytes
5355705
matrix file size mb
5.11
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=2718; raw_genes=22447; leiden_clusters=18; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated