HCC-090-09-1H
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-090-09-1H, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
19Clusters
20,555Expressed genes
4280Mean UMI
1180Mean genes
7.142Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 19 | 0.6303 | 2.3674 | 8 |
| Myeloid_APC | 19 | 0.526 | 1.7899 | 9 |
| T_NK_cytotoxic | 19 | 0.3119 | 1.2096 | 10 |
| Endothelial | 19 | 0.2488 | 1.3223 | 7 |
| Proliferation | 19 | 0.1178 | 1.1994 | 7 |
| Fibroblast_stroma | 19 | 0.0801 | 1.1428 | 8 |
| Epithelial_tumor | 19 | 0.0799 | 1.1657 | 6 |
| Checkpoint_exhaustion | 19 | 0.0697 | 0.128 | 8 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 325 | 2581.4923 | 872 | 7.5096 |
| cluster_2 | 220 | 2498.2682 | 767 | 7.3362 |
| cluster_3 | 202 | 9081.3911 | 961.5 | 3.5034 |
| cluster_4 | 198 | 2629.4242 | 933 | 7.6726 |
| cluster_5 | 179 | 4851.2905 | 1362 | 7.6754 |
| cluster_6 | 158 | 5444.8354 | 1414 | 8.2224 |
| cluster_7 | 107 | 7016.3832 | 1669 | 7.8999 |
| cluster_9 | 98 | 2675.949 | 1006.5 | 5.9546 |
| cluster_8 | 98 | 2794.898 | 873.5 | 8.7198 |
| cluster_10 | 92 | 2665.7826 | 981.5 | 8.1731 |
| cluster_11 | 68 | 4645.0588 | 1558 | 6.3195 |
| cluster_12 | 66 | 4541.0758 | 1599.5 | 6.8035 |
| cluster_13 | 53 | 6810.7547 | 1612 | 7.0178 |
| cluster_14 | 36 | 3094.4444 | 892.5 | 7.3617 |
| cluster_15 | 31 | 3577.3871 | 1577 | 8.6149 |
| cluster_16 | 25 | 5008.12 | 1756 | 6.2713 |
| cluster_17 | 23 | 6011.4348 | 1317 | 7.957 |
| cluster_18 | 11 | 4480.3636 | 1579 | 8.9811 |
| cluster_19 | 10 | 4315.3 | 1365.5 | 7.323 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_14 | 1 | TPSAB1 | 4.7225 | 4.7465 | 1 |
| cluster_3 | 1 | IGKC | 4.4317 | 5.6853 | 0.9752 |
| cluster_19 | 1 | FABP4 | 4.3097 | 4.3488 | 1 |
| cluster_16 | 1 | MGP | 4.1659 | 4.3559 | 1 |
| cluster_18 | 1 | TAGLN | 3.7158 | 3.7726 | 1 |
| cluster_17 | 1 | CST3 | 3.704 | 4.7367 | 1 |
| cluster_5 | 1 | S100A9 | 3.506 | 4.0449 | 0.9721 |
| cluster_7 | 1 | HLA-DRA | 3.226 | 4.5187 | 1 |
| cluster_6 | 1 | HLA-DRA | 3.2218 | 4.4325 | 1 |
| cluster_11 | 1 | MGP | 2.6258 | 2.7786 | 0.9559 |
| cluster_15 | 1 | TM4SF4 | 2.5948 | 2.6552 | 1 |
| cluster_12 | 1 | DNASE1L3 | 2.5169 | 2.5908 | 1 |
| cluster_9 | 1 | S100A9 | 2.4747 | 3.2061 | 0.9898 |
| cluster_13 | 1 | STMN1 | 2.1543 | 2.3277 | 0.9623 |
| cluster_4 | 1 | NKG7 | 2.1059 | 2.7968 | 1 |
| cluster_1 | 1 | CCL5 | 1.7958 | 3.0661 | 0.9754 |
| cluster_10 | 1 | CCL4 | 1.7847 | 2.985 | 0.9783 |
| cluster_2 | 1 | IL7R | 1.5669 | 2.0936 | 0.9591 |
| cluster_8 | 1 | MS4A1 | 1.4316 | 1.4857 | 0.9082 |
| cluster_14 | 2 | TPSB2 | 4.58 | 4.607 | 1 |
| cluster_3 | 2 | IGHG1 | 3.6809 | 4.1462 | 0.8713 |
| cluster_16 | 2 | DEPP1 | 3.5559 | 3.6312 | 1 |
| cluster_5 | 2 | LYZ | 3.4869 | 4.0559 | 1 |
| cluster_18 | 2 | ACTA2 | 3.4215 | 3.4529 | 1 |
| cluster_17 | 2 | HLA-DRA | 3.3339 | 4.7609 | 1 |
| cluster_6 | 2 | CST3 | 3.0426 | 3.8775 | 0.9937 |
| cluster_7 | 2 | CD74 | 2.9455 | 4.7419 | 1 |
| cluster_19 | 2 | IGFBP7 | 2.7571 | 3.062 | 1 |
| cluster_11 | 2 | SPARCL1 | 2.5695 | 2.6374 | 0.9706 |
| cluster_12 | 2 | IGFBP7 | 2.4797 | 2.7165 | 0.9848 |
| cluster_15 | 2 | ANXA4 | 2.2591 | 2.3798 | 1 |
| cluster_9 | 2 | S100A8 | 2.2513 | 2.8205 | 0.9796 |
| cluster_13 | 2 | HIST1H4C | 2.0745 | 2.3739 | 0.9245 |
| cluster_4 | 2 | GNLY | 1.9974 | 2.2262 | 0.9394 |
| cluster_10 | 2 | CCL3 | 1.7271 | 2.0902 | 0.8261 |
| cluster_8 | 2 | CD74 | 1.215 | 3.1095 | 1 |
| cluster_1 | 2 | RGS1 | 1.074 | 2.7759 | 0.9385 |
| cluster_2 | 2 | CD52 | 0.8046 | 2.2381 | 0.9773 |
| cluster_14 | 3 | CPA3 | 3.6643 | 3.6711 | 1 |
| cluster_18 | 3 | IGFBP7 | 3.3682 | 3.6683 | 1 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-090-09-1H
Sample ID
HCC-090-09-1H
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
3,136
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-090-09-1H.counts.matrix.tsv.gz (5.09 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=3136; raw genes=21626; Leiden clusters=19; 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-090-09-1H
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-090-09-1H.counts.matrix.tsv.gz
matrix file size bytes
5341083
matrix file size mb
5.09
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=3136; raw_genes=21626; leiden_clusters=19; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated