HCC-090-07-1H
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-090-07-1H, generated 2026-07-09 12:54:49 +0800.
1,810Cells analyzed
21Clusters
18,432Expressed genes
3369Mean UMI
1088Mean genes
5.718Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| B_plasma | 21 | 0.5663 | 2.2869 | 8 |
| Myeloid_APC | 21 | 0.4815 | 1.9709 | 9 |
| T_NK_cytotoxic | 21 | 0.3257 | 1.1884 | 10 |
| Endothelial | 21 | 0.1824 | 1.1383 | 7 |
| Proliferation | 21 | 0.0943 | 1.2462 | 7 |
| Checkpoint_exhaustion | 21 | 0.0828 | 0.3222 | 8 |
| Fibroblast_stroma | 21 | 0.0796 | 1.2399 | 6 |
| Epithelial_tumor | 21 | 0.0648 | 1.1447 | 6 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 359 | 1847.7493 | 793 | 4.9734 |
| cluster_2 | 210 | 7635.3381 | 687 | 1.8677 |
| cluster_3 | 207 | 4522.1546 | 1430 | 8.0061 |
| cluster_4 | 165 | 2000.3515 | 875 | 6.147 |
| cluster_5 | 158 | 2008.7215 | 921.5 | 6.2213 |
| cluster_6 | 140 | 3667.2 | 1335 | 7.1078 |
| cluster_7 | 88 | 3950.0341 | 1518.5 | 6.2989 |
| cluster_8 | 82 | 2042.3171 | 921 | 5.2752 |
| cluster_9 | 77 | 2088.4416 | 795 | 7.4547 |
| cluster_10 | 76 | 1989.75 | 872.5 | 4.2736 |
| cluster_11 | 45 | 3428.7333 | 1442 | 6.3359 |
| cluster_12 | 39 | 4436.5897 | 1530 | 6.942 |
| cluster_13 | 36 | 2206.6667 | 994 | 6.7749 |
| cluster_14 | 28 | 4712.5 | 1499.5 | 6.4884 |
| cluster_15 | 22 | 5063.0909 | 1653 | 6.0517 |
| cluster_16 | 20 | 3514.85 | 1525 | 8.5841 |
| cluster_17 | 15 | 2391.5333 | 867 | 5.0656 |
| cluster_18 | 15 | 2316.5333 | 1033 | 5.7793 |
| cluster_19 | 11 | 3845.4545 | 1335 | 7.1345 |
| cluster_20 | 9 | 3622.4444 | 1483 | 8.5669 |
| cluster_21 | 8 | 5118 | 1811 | 4.1064 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_2 | 1 | IGKC | 5.7817 | 6.6063 | 0.9905 |
| cluster_17 | 1 | TPSB2 | 5.1783 | 5.1849 | 1 |
| cluster_21 | 1 | MGP | 4.0561 | 4.2132 | 1 |
| cluster_14 | 1 | CST3 | 3.9989 | 4.9689 | 1 |
| cluster_20 | 1 | C11orf96 | 3.7926 | 3.9841 | 1 |
| cluster_15 | 1 | C1QB | 3.6403 | 3.7358 | 1 |
| cluster_3 | 1 | CST3 | 3.4493 | 4.0868 | 1 |
| cluster_19 | 1 | CXCL10 | 3.1141 | 3.1431 | 0.9091 |
| cluster_6 | 1 | S100A8 | 2.9804 | 3.2624 | 0.9857 |
| cluster_12 | 1 | HIST1H4C | 2.896 | 3.3188 | 0.9744 |
| cluster_13 | 1 | DNASE1L3 | 2.8211 | 2.9487 | 1 |
| cluster_7 | 1 | MGP | 2.6661 | 2.7115 | 0.9773 |
| cluster_16 | 1 | CLU | 2.6575 | 2.8796 | 1 |
| cluster_10 | 1 | S100A9 | 2.5485 | 2.9862 | 0.9737 |
| cluster_11 | 1 | PRSS23 | 2.3807 | 2.462 | 1 |
| cluster_4 | 1 | CCL5 | 1.9721 | 3.1888 | 0.9818 |
| cluster_5 | 1 | CCL4 | 1.7441 | 2.714 | 0.9873 |
| cluster_9 | 1 | MS4A1 | 1.6634 | 1.6886 | 0.961 |
| cluster_8 | 1 | CCL5 | 1.6591 | 2.9804 | 1 |
| cluster_1 | 1 | IL7R | 1.5431 | 1.7699 | 0.9443 |
| cluster_18 | 1 | TRBC2 | 1.4992 | 2.1312 | 1 |
| cluster_2 | 2 | IGHG3 | 5.6532 | 5.9433 | 0.9429 |
| cluster_17 | 2 | TPSAB1 | 4.6025 | 4.6052 | 1 |
| cluster_20 | 2 | TAGLN | 3.7822 | 3.8266 | 1 |
| cluster_14 | 2 | CD74 | 3.5129 | 5.5834 | 1 |
| cluster_15 | 2 | FTL | 3.4448 | 5.4087 | 1 |
| cluster_21 | 2 | CLU | 3.2274 | 3.4647 | 1 |
| cluster_3 | 2 | CD74 | 3.216 | 4.973 | 1 |
| cluster_6 | 2 | LYZ | 2.9785 | 3.399 | 1 |
| cluster_19 | 2 | GBP1 | 2.9555 | 3.1164 | 1 |
| cluster_13 | 2 | CTSL | 2.6609 | 2.7559 | 1 |
| cluster_7 | 2 | ADIRF | 2.6372 | 2.7094 | 1 |
| cluster_16 | 2 | TM4SF4 | 2.4537 | 2.4646 | 1 |
| cluster_12 | 2 | TUBA1B | 2.3474 | 2.7625 | 1 |
| cluster_10 | 2 | S100A8 | 2.3294 | 2.7441 | 0.9474 |
| cluster_11 | 2 | RAMP3 | 2.2305 | 2.2908 | 0.9778 |
| cluster_4 | 2 | GNLY | 1.9542 | 2.1951 | 0.9212 |
| cluster_5 | 2 | CCL3 | 1.5367 | 1.8397 | 0.8734 |
| cluster_18 | 2 | TRAC | 1.4748 | 1.8092 | 1 |
| cluster_9 | 2 | CD74 | 1.4696 | 3.5319 | 1 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
HCC-090-07-1H
Sample ID
HCC-090-07-1H
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
1,810
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-090-07-1H.counts.matrix.tsv.gz (2.78 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=1810; raw genes=18684; Leiden clusters=21; 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-090-07-1H
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-090-07-1H.counts.matrix.tsv.gz
matrix file size bytes
2916821
matrix file size mb
2.78
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=1810; raw_genes=18684; leiden_clusters=21; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated