HCC-059-01-1A
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-059-01-1A, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
17Clusters
24,572Expressed genes
6085Mean UMI
1929Mean genes
2.848Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 17 | 0.4918 | 2.4783 | 8 |
| Myeloid_APC | 17 | 0.3755 | 1.4372 | 9 |
| T_NK_cytotoxic | 17 | 0.3344 | 1.2993 | 10 |
| Checkpoint_exhaustion | 17 | 0.1933 | 0.8515 | 8 |
| Fibroblast_stroma | 17 | 0.164 | 1.3718 | 8 |
| Proliferation | 17 | 0.1256 | 1.2446 | 7 |
| Endothelial | 17 | 0.0752 | 0.5151 | 7 |
| Epithelial_tumor | 17 | 0.0326 | 0.2748 | 7 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 357 | 6458.9944 | 2457 | 3.4685 |
| cluster_2 | 344 | 7192.4128 | 2339.5 | 3.6636 |
| cluster_3 | 314 | 1983.7548 | 805 | 1.4674 |
| cluster_4 | 238 | 2250.7101 | 862 | 1.3315 |
| cluster_5 | 223 | 8572.6502 | 2867 | 3.5995 |
| cluster_6 | 122 | 1903.8443 | 524.5 | 3.0501 |
| cluster_7 | 71 | 8807.6197 | 2846 | 3.3148 |
| cluster_8 | 67 | 12171.7463 | 2649 | 3.9615 |
| cluster_9 | 53 | 13488.8868 | 3466 | 4.5054 |
| cluster_10 | 47 | 4297.766 | 1515 | 1.421 |
| cluster_11 | 38 | 5191.4737 | 1237 | 2.7886 |
| cluster_12 | 37 | 27058.4595 | 2876 | 1.6926 |
| cluster_13 | 30 | 3007.4333 | 1023 | 2.2216 |
| cluster_14 | 25 | 7834.32 | 2674 | 3.6759 |
| cluster_15 | 13 | 6217.2308 | 2245 | 2.8657 |
| cluster_16 | 13 | 6298.3846 | 2200 | 3.2345 |
| cluster_17 | 8 | 10353.125 | 3734 | 4.1248 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_12 | 1 | IGHG4 | 6.0624 | 6.9008 | 1 |
| cluster_16 | 1 | MT2A | 4.0823 | 4.7812 | 1 |
| cluster_10 | 1 | APOA2 | 2.8727 | 3.4378 | 0.9574 |
| cluster_9 | 1 | FTL | 2.8482 | 5.1817 | 1 |
| cluster_14 | 1 | HLA-DRA | 2.5429 | 3.09 | 1 |
| cluster_8 | 1 | TIMP1 | 2.4203 | 2.8448 | 0.8358 |
| cluster_11 | 1 | COL1A1 | 2.3778 | 2.5348 | 0.9211 |
| cluster_7 | 1 | CXCL13 | 2.3266 | 2.3531 | 0.8169 |
| cluster_3 | 1 | CXCL8 | 2.3048 | 3.1006 | 0.9809 |
| cluster_4 | 1 | G0S2 | 2.2761 | 2.931 | 0.979 |
| cluster_1 | 1 | CCL5 | 2.2707 | 2.6472 | 0.9888 |
| cluster_17 | 1 | HIST1H4C | 2.1334 | 2.6495 | 0.875 |
| cluster_15 | 1 | CXCL8 | 2.0649 | 3.2091 | 1 |
| cluster_5 | 1 | IKZF2 | 2.0483 | 2.1534 | 0.9641 |
| cluster_2 | 1 | IL7R | 1.873 | 2.5204 | 0.9506 |
| cluster_13 | 1 | IGFBP7 | 1.4464 | 1.6173 | 0.8333 |
| cluster_6 | 1 | IGKC | 0.5888 | 1.5429 | 0.8525 |
| cluster_12 | 2 | IGHG1 | 6.024 | 6.3204 | 0.973 |
| cluster_16 | 2 | MT1X | 3.9997 | 4.1972 | 1 |
| cluster_9 | 2 | HLA-DRA | 2.8383 | 3.3421 | 1 |
| cluster_10 | 2 | ALB | 2.8219 | 4.2616 | 1 |
| cluster_4 | 2 | S100A8 | 2.2304 | 2.5406 | 0.9496 |
| cluster_1 | 2 | NKG7 | 2.2248 | 2.4279 | 0.9664 |
| cluster_14 | 2 | CD74 | 2.2207 | 3.1586 | 1 |
| cluster_11 | 2 | IGFBP7 | 2.1604 | 2.312 | 1 |
| cluster_8 | 2 | IFI30 | 2.024 | 2.368 | 0.8358 |
| cluster_5 | 2 | IL12RB2 | 2.0132 | 2.1899 | 0.8744 |
| cluster_3 | 2 | DOCK4 | 1.9127 | 2.5335 | 0.9682 |
| cluster_17 | 2 | HMGB2 | 1.8106 | 2.1923 | 0.875 |
| cluster_7 | 2 | TOX | 1.7531 | 2.0721 | 0.9296 |
| cluster_2 | 2 | RPS29 | 1.5177 | 3.4006 | 0.968 |
| cluster_15 | 2 | NAMPT | 1.378 | 2.9564 | 1 |
| cluster_13 | 2 | SPARC | 1.1646 | 1.3132 | 0.9 |
| cluster_6 | 2 | IGLC1 | 0.5406 | 0.7992 | 0.4918 |
| cluster_12 | 3 | IGKC | 4.2063 | 5.1184 | 1 |
| cluster_16 | 3 | MT1E | 2.9448 | 3.0708 | 0.9231 |
| cluster_9 | 3 | CD74 | 2.7272 | 3.6206 | 0.9811 |
| cluster_10 | 3 | FABP1 | 2.6491 | 2.9901 | 1 |
| cluster_1 | 3 | GNLY | 2.2186 | 2.3549 | 0.902 |
| cluster_11 | 3 | COL1A2 | 2.0709 | 2.2046 | 0.9211 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-059-01-1A
Sample ID
HCC-059-01-1A
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
7,194
Analysis Status
Matrix available; UMAP generated
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-059-01-1A.counts.matrix.tsv.gz (17.19 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=7194; raw genes=27788; Leiden clusters=17; 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-059-01-1A
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 available
matrix file name
HCC-059-01-1A.counts.matrix.tsv.gz
matrix file size bytes
18024036
matrix file size mb
17.19
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=7194; raw_genes=27788; leiden_clusters=17; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated