HCC-090-06-1H
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-090-06-1H, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
20Clusters
21,974Expressed genes
7607Mean UMI
1759Mean genes
6.606Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 20 | 1.2452 | 2.7707 | 8 |
| Myeloid_APC | 20 | 1.069 | 2.6201 | 9 |
| T_NK_cytotoxic | 20 | 0.3515 | 1.3145 | 10 |
| Proliferation | 20 | 0.141 | 1.476 | 7 |
| Checkpoint_exhaustion | 20 | 0.0985 | 0.1824 | 8 |
| Endothelial | 20 | 0.0936 | 0.752 | 7 |
| Epithelial_tumor | 20 | 0.0713 | 0.8207 | 7 |
| Fibroblast_stroma | 20 | 0.0155 | 0.0455 | 7 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 336 | 7967.0804 | 2008 | 7.6679 |
| cluster_2 | 247 | 11075.9838 | 2465 | 6.9709 |
| cluster_3 | 237 | 10475.8861 | 1083 | 3.7238 |
| cluster_4 | 228 | 7478.2544 | 1915.5 | 7.2653 |
| cluster_5 | 186 | 3800.1613 | 1318.5 | 7.5169 |
| cluster_6 | 165 | 3862.2606 | 1247 | 6.0687 |
| cluster_7 | 96 | 8259.1771 | 1993 | 7.7754 |
| cluster_8 | 72 | 4339.125 | 1303.5 | 7.5619 |
| cluster_9 | 69 | 10405.5652 | 1054 | 3.5221 |
| cluster_10 | 65 | 8736.4923 | 2078 | 6.937 |
| cluster_11 | 49 | 10227.0204 | 2563 | 7.0231 |
| cluster_12 | 48 | 5791.7083 | 1733.5 | 5.977 |
| cluster_13 | 48 | 4016.1042 | 1302 | 5.5071 |
| cluster_14 | 47 | 4926.7447 | 1636 | 7.1037 |
| cluster_15 | 34 | 4109.2353 | 1448.5 | 7.405 |
| cluster_16 | 24 | 6582.875 | 1884.5 | 7.0407 |
| cluster_17 | 18 | 5834.9444 | 1767.5 | 8.0839 |
| cluster_18 | 17 | 8407.1176 | 1923 | 7.2708 |
| cluster_19 | 10 | 10052.7 | 1189.5 | 4.3503 |
| cluster_20 | 4 | 7269.25 | 1932 | 7.1275 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_9 | 1 | IGLC2 | 6.3535 | 7.3317 | 1 |
| cluster_3 | 1 | IGKC | 4.8245 | 7.3207 | 1 |
| cluster_20 | 1 | TPSB2 | 4.5626 | 4.5762 | 1 |
| cluster_19 | 1 | IGHG4 | 4.392 | 6.7429 | 1 |
| cluster_2 | 1 | C1QB | 3.7621 | 4.5839 | 1 |
| cluster_4 | 1 | S100A9 | 3.0263 | 3.7212 | 0.9912 |
| cluster_11 | 1 | STMN1 | 2.7478 | 2.9439 | 1 |
| cluster_18 | 1 | CXCL9 | 2.5129 | 2.5646 | 0.8824 |
| cluster_15 | 1 | CCL5 | 2.4506 | 3.731 | 1 |
| cluster_10 | 1 | WDFY4 | 2.4503 | 2.6923 | 1 |
| cluster_16 | 1 | ALB | 2.4466 | 2.9539 | 1 |
| cluster_12 | 1 | GZMB | 2.3798 | 2.4804 | 0.9375 |
| cluster_14 | 1 | IFI27 | 2.2932 | 2.6932 | 0.9574 |
| cluster_13 | 1 | S100A9 | 2.272 | 3.2573 | 1 |
| cluster_8 | 1 | MS4A1 | 2.2444 | 2.2893 | 0.9861 |
| cluster_1 | 1 | HLA-DRA | 2.2208 | 4.9105 | 1 |
| cluster_17 | 1 | ANXA4 | 2.1709 | 2.4311 | 1 |
| cluster_7 | 1 | HLA-DRA | 2.0837 | 5.0465 | 1 |
| cluster_6 | 1 | CCL5 | 2.0704 | 3.2216 | 0.9333 |
| cluster_5 | 1 | NKG7 | 1.9642 | 2.5955 | 1 |
| cluster_9 | 2 | IGLC3 | 5.0693 | 5.441 | 1 |
| cluster_19 | 2 | IGHG1 | 4.326 | 6.2045 | 1 |
| cluster_3 | 2 | IGHG1 | 3.9745 | 5.4037 | 0.9916 |
| cluster_20 | 2 | CPA3 | 3.8463 | 3.8491 | 1 |
| cluster_2 | 2 | C1QC | 3.5024 | 4.0636 | 1 |
| cluster_4 | 2 | S100A8 | 2.7001 | 3.2378 | 0.9561 |
| cluster_11 | 2 | TUBA1B | 2.577 | 3.5204 | 1 |
| cluster_10 | 2 | CPVL | 2.3353 | 3.3155 | 1 |
| cluster_13 | 2 | S100A8 | 2.2582 | 3.0495 | 0.9792 |
| cluster_14 | 2 | IGFBP7 | 2.2404 | 2.3562 | 0.9149 |
| cluster_15 | 2 | NKG7 | 2.2123 | 2.9887 | 1 |
| cluster_1 | 2 | HLA-DPB1 | 2.2057 | 4.0331 | 1 |
| cluster_18 | 2 | HLA-DQA1 | 2.1717 | 3.7239 | 1 |
| cluster_17 | 2 | CLU | 2.1011 | 2.25 | 1 |
| cluster_16 | 2 | APOA2 | 2.0882 | 2.2816 | 0.9583 |
| cluster_7 | 2 | HLA-DPB1 | 1.9419 | 4.0467 | 1 |
| cluster_5 | 2 | CD69 | 1.9346 | 2.9593 | 0.9839 |
| cluster_8 | 2 | CD52 | 1.8737 | 3.2647 | 1 |
| cluster_12 | 2 | PTGDS | 1.7774 | 1.8032 | 0.6042 |
| cluster_6 | 2 | CD69 | 1.4863 | 2.5683 | 0.9636 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-090-06-1H
Sample ID
HCC-090-06-1H
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
5,451
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-090-06-1H.counts.matrix.tsv.gz (11.62 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=5451; raw genes=23933; Leiden clusters=20; 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-090-06-1H
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-090-06-1H.counts.matrix.tsv.gz
matrix file size bytes
12187460
matrix file size mb
11.62
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=5451; raw_genes=23933; leiden_clusters=20; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated