HCC-059-02-1A
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-059-02-1A, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
10Clusters
18,958Expressed genes
1195Mean genes
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| Myeloid_APC | 10 | 0.3835 | 2.0498 | 9 |
| B_plasma | 10 | 0.2844 | 0.8264 | 6 |
| Endothelial | 10 | 0.1712 | 0.9122 | 4 |
| T_NK_cytotoxic | 10 | 0.1568 | 0.6081 | 9 |
| Fibroblast_stroma | 10 | 0.1013 | 0.8677 | 7 |
| Checkpoint_exhaustion | 10 | 0.0947 | 0.2471 | 8 |
| Proliferation | 10 | 0.0538 | 0.2232 | 3 |
| Epithelial_tumor | 10 | 0.0113 | 0.0579 | 6 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_2 | 494 | 765.5 | ||
| cluster_6 | 420 | 1205.5 | ||
| cluster_4 | 405 | 1006 | ||
| cluster_7 | 181 | 2310 | ||
| cluster_8 | 129 | 886 | ||
| cluster_10 | 124 | 1230.5 | ||
| cluster_9 | 87 | 721 | ||
| cluster_1 | 75 | 1818 | ||
| cluster_5 | 56 | 1131 | ||
| cluster_3 | 29 | 343 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_7 | 1 | HLA-DRA | 3.7963 | 4.496 | 1 |
| cluster_3 | 1 | CXCL8 | 2.8414 | 2.9681 | 1 |
| cluster_1 | 1 | FLT1 | 2.491 | 2.6208 | 0.9733 |
| cluster_5 | 1 | IGFBP7 | 2.3813 | 2.6564 | 1 |
| cluster_8 | 1 | GNLY | 1.9985 | 2.0458 | 0.938 |
| cluster_10 | 1 | HLA-DRA | 1.6529 | 2.5937 | 0.9597 |
| cluster_9 | 1 | IGFBP7 | 1.3423 | 1.6257 | 0.908 |
| cluster_4 | 1 | HSP90AA1 | 1.2066 | 3.6806 | 1 |
| cluster_6 | 1 | S100A4 | 0.913 | 1.57 | 0.8833 |
| cluster_2 | 1 | APOA2 | 0.2182 | 0.9773 | 0.747 |
| cluster_7 | 2 | CD74 | 3.4666 | 4.423 | 1 |
| cluster_1 | 2 | MAGI1 | 2.4333 | 2.5363 | 0.9467 |
| cluster_5 | 2 | PRKG1 | 2.0484 | 2.0698 | 0.8929 |
| cluster_3 | 2 | NAMPT | 1.7987 | 2.3939 | 1 |
| cluster_10 | 2 | CD74 | 1.6521 | 2.8197 | 0.9919 |
| cluster_9 | 2 | CALCRL | 1.2289 | 1.3986 | 0.8506 |
| cluster_4 | 2 | CCL20 | 1.1621 | 1.4376 | 0.6173 |
| cluster_8 | 2 | ZEB2 | 0.7785 | 1.246 | 0.8062 |
| cluster_6 | 2 | IKZF2 | 0.7375 | 0.8734 | 0.5429 |
| cluster_2 | 2 | ANK3 | 0.1921 | 0.3162 | 0.2834 |
| cluster_7 | 3 | HLA-DPA1 | 3.3421 | 3.8883 | 1 |
| cluster_1 | 3 | GRB10 | 2.3497 | 2.4388 | 0.9733 |
| cluster_5 | 3 | CALD1 | 1.9626 | 2.0516 | 0.9643 |
| cluster_3 | 3 | G0S2 | 1.3416 | 1.5119 | 0.931 |
| cluster_10 | 3 | CD83 | 1.3198 | 1.7496 | 0.879 |
| cluster_9 | 3 | PLPP1 | 1.2063 | 1.4375 | 0.7701 |
| cluster_4 | 3 | SIK3 | 1.0899 | 2.1248 | 0.9407 |
| cluster_8 | 3 | CD247 | 0.7688 | 1.106 | 0.814 |
| cluster_6 | 3 | IL32 | 0.7358 | 1.2278 | 0.731 |
| cluster_2 | 3 | ALB | 0.1795 | 1.9278 | 0.9879 |
| cluster_7 | 4 | C1QB | 3.1374 | 3.2708 | 0.989 |
| cluster_1 | 4 | LDB2 | 2.3388 | 2.4456 | 1 |
| cluster_5 | 4 | TAGLN | 1.8043 | 1.8242 | 0.8393 |
| cluster_9 | 4 | FLT1 | 1.1817 | 1.3535 | 0.7356 |
| cluster_3 | 4 | SOD2 | 1.1458 | 1.6167 | 0.8966 |
| cluster_10 | 4 | HLA-DPA1 | 1.0608 | 1.8437 | 0.8871 |
| cluster_4 | 4 | KLRB1 | 0.9404 | 1.2993 | 0.7506 |
| cluster_8 | 4 | GZMB | 0.7196 | 0.7438 | 0.6357 |
| cluster_6 | 4 | AL136456.1 | 0.6834 | 0.9949 | 0.6071 |
| cluster_2 | 4 | ALDOB | 0.178 | 0.3618 | 0.3117 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-059-02-1A
Sample ID
HCC-059-02-1A
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 (10X Genomics)
Cell Count
12,871
Analysis Status
Matrix available; UMAP generated by fallback sampled pipeline
UMAP Status
Ready
Metadata / Source Notes
Project ID: HCC-059; Cancer type: Hepatocellular Cancer; Source: NCBI (GEO); Accession: GSE202642; Country: CHN; Sample type: Tumour; Protocol: 10X Genomics; Matrix: HCC-059-02-1A.counts.matrix.tsv.gz (19.77 MB); Matrix integrity: gzip file ended before end-of-stream marker during UMAP generation; redownload required before UMAP can be generated.; 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-059-02-1A
source reference
CancerSCEM 2.0 metadata table; data source=NCBI (GEO); accession=GSE202642; downloaded 2026-07-06
data accession
GSE202642
project id
HCC-059
sample type
Tumour
country
CHN
data source
NCBI (GEO)
accession no
GSE202642
construction protocol
10X Genomics
transcriptome profile
Yes
metabolic profile
Yes
matrix status
Matrix incomplete; redownload required
matrix file name
HCC-059-02-1A.counts.matrix.tsv.gz
matrix file size bytes
20725505
matrix file size mb
19.77
umap coordinates url
umap summary url
umap pipeline
Fallback Python normalize_total/log1p/HVG/SVD/UMAP; sampled 3000/12871 cells; generated 2026-07-09
matrix integrity status
Gzip EOF/truncated during UMAP generation