HCC-090-05-1H
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-090-05-1H, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
19Clusters
20,435Expressed genes
4343Mean UMI
1394Mean genes
6.833Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 19 | 0.9193 | 2.4165 | 8 |
| Myeloid_APC | 19 | 0.7841 | 2.5248 | 9 |
| Endothelial | 19 | 0.1307 | 0.643 | 7 |
| Proliferation | 19 | 0.1288 | 0.9264 | 7 |
| Epithelial_tumor | 19 | 0.099 | 1.5265 | 6 |
| T_NK_cytotoxic | 19 | 0.0903 | 0.5933 | 10 |
| Checkpoint_exhaustion | 19 | 0.0527 | 0.1605 | 8 |
| Fibroblast_stroma | 19 | 0.0093 | 0.102 | 7 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 299 | 2378.9264 | 1098 | 6.6651 |
| cluster_2 | 282 | 4049.4326 | 1393 | 7.2784 |
| cluster_3 | 239 | 4962.8996 | 928 | 6.938 |
| cluster_4 | 220 | 5131.5773 | 1563.5 | 7.7193 |
| cluster_5 | 162 | 3740.2469 | 1421.5 | 6.7012 |
| cluster_6 | 144 | 8186.9444 | 2298 | 7.1611 |
| cluster_7 | 114 | 2489.7105 | 923 | 6.9 |
| cluster_8 | 95 | 5836.6105 | 1692 | 6.9012 |
| cluster_9 | 79 | 9357.8481 | 2109 | 7.2152 |
| cluster_10 | 73 | 3100.3836 | 1069 | 7.6947 |
| cluster_11 | 64 | 3083.3281 | 1273 | 5.8223 |
| cluster_12 | 59 | 2195.7797 | 777 | 4.2497 |
| cluster_13 | 48 | 4812.0417 | 740 | 4.3183 |
| cluster_14 | 36 | 2784.0278 | 1332.5 | 7.4807 |
| cluster_15 | 25 | 2273.4 | 1049 | 5.1971 |
| cluster_16 | 20 | 3812.2 | 1166.5 | 7.14 |
| cluster_17 | 19 | 2866.8947 | 1315 | 5.3923 |
| cluster_18 | 14 | 4733.1429 | 405 | 3.7147 |
| cluster_19 | 8 | 2153.5 | 816.5 | 5.8719 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_18 | 1 | HBB | 7.0171 | 7.262 | 1 |
| cluster_13 | 1 | IGHG3 | 6.1248 | 6.4901 | 1 |
| cluster_19 | 1 | TPSB2 | 5.2179 | 5.2272 | 1 |
| cluster_6 | 1 | C1QB | 3.9625 | 4.3586 | 0.9931 |
| cluster_9 | 1 | IGKC | 3.844 | 5.8159 | 0.9873 |
| cluster_3 | 1 | IGKC | 3.4958 | 5.2017 | 0.9958 |
| cluster_5 | 1 | S100A8 | 3.3863 | 4.6398 | 1 |
| cluster_12 | 1 | S100A8 | 3.2903 | 4.721 | 1 |
| cluster_8 | 1 | CST3 | 3.2897 | 4.9162 | 1 |
| cluster_1 | 1 | DNASE1L3 | 2.9709 | 3.2903 | 0.9967 |
| cluster_17 | 1 | GZMB | 2.6408 | 2.6804 | 1 |
| cluster_14 | 1 | KRT18 | 2.6015 | 2.6219 | 0.9167 |
| cluster_4 | 1 | HLA-DRA | 2.5283 | 4.1303 | 0.9955 |
| cluster_11 | 1 | TM4SF1 | 2.5127 | 2.8022 | 0.9375 |
| cluster_16 | 1 | MS4A1 | 2.3591 | 2.3707 | 1 |
| cluster_15 | 1 | DNASE1L3 | 2.191 | 2.9272 | 1 |
| cluster_2 | 1 | FCN1 | 2.068 | 2.4768 | 0.9858 |
| cluster_7 | 1 | CCL4 | 1.4244 | 2.2494 | 0.9035 |
| cluster_10 | 1 | CCL5 | 1.4038 | 1.6615 | 0.7123 |
| cluster_18 | 2 | HBA2 | 6.6723 | 6.8244 | 1 |
| cluster_13 | 2 | IGHG4 | 5.8263 | 6.2738 | 1 |
| cluster_19 | 2 | TPSAB1 | 4.7058 | 4.7114 | 1 |
| cluster_6 | 2 | MARCO | 3.8321 | 3.9452 | 0.9792 |
| cluster_5 | 2 | S100A9 | 3.2636 | 4.4894 | 1 |
| cluster_3 | 2 | JCHAIN | 3.1684 | 3.7366 | 0.9833 |
| cluster_8 | 2 | CD74 | 3.1457 | 5.8646 | 1 |
| cluster_9 | 2 | JCHAIN | 3.1377 | 3.9606 | 0.962 |
| cluster_12 | 2 | S100A9 | 2.9841 | 4.3863 | 1 |
| cluster_1 | 2 | FCN3 | 2.736 | 2.8708 | 0.99 |
| cluster_14 | 2 | KRT8 | 2.4549 | 2.4701 | 0.9722 |
| cluster_11 | 2 | EMP1 | 2.4321 | 2.5055 | 0.8281 |
| cluster_4 | 2 | CD74 | 2.3331 | 4.9447 | 1 |
| cluster_15 | 2 | FCN3 | 2.0111 | 2.5299 | 1 |
| cluster_2 | 2 | S100A4 | 1.9136 | 2.7567 | 0.9965 |
| cluster_16 | 2 | CD52 | 1.6925 | 2.5923 | 0.95 |
| cluster_17 | 2 | CD74 | 1.6293 | 4.4821 | 1 |
| cluster_7 | 2 | CCL5 | 1.3223 | 1.5559 | 0.7456 |
| cluster_10 | 2 | HIST1H4C | 1.2338 | 1.8937 | 0.8356 |
| cluster_18 | 3 | HBA1 | 6.4958 | 6.6009 | 1 |
| cluster_13 | 3 | IGHG1 | 4.6236 | 5.3591 | 1 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-090-05-1H
Sample ID
HCC-090-05-1H
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
2,399
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-090-05-1H.counts.matrix.tsv.gz (4.42 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=2399; raw genes=21064; 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-090-05-1H
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-090-05-1H.counts.matrix.tsv.gz
matrix file size bytes
4635670
matrix file size mb
4.42
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=2399; raw_genes=21064; leiden_clusters=19; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated