iCCA-066-04-1A
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 iCCA-066-04-1A, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
10Clusters
16,848Expressed genes
1566Mean genes
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| Fibroblast_stroma | 10 | 0.7278 | 2.7538 | 7 |
| Myeloid_APC | 10 | 0.7273 | 2.565 | 9 |
| B_plasma | 10 | 0.4474 | 1.0805 | 6 |
| T_NK_cytotoxic | 10 | 0.154 | 0.855 | 9 |
| Proliferation | 10 | 0.1264 | 0.29 | 3 |
| Endothelial | 10 | 0.1128 | 0.286 | 4 |
| Epithelial_tumor | 10 | 0.0758 | 0.4422 | 6 |
| Checkpoint_exhaustion | 10 | 0.0647 | 0.1568 | 8 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_2 | 479 | 1056 | ||
| cluster_5 | 295 | 855 | ||
| cluster_6 | 261 | 1334 | ||
| cluster_4 | 241 | 2886 | ||
| cluster_1 | 234 | 1027 | ||
| cluster_7 | 203 | 2870 | ||
| cluster_10 | 80 | 1441 | ||
| cluster_3 | 79 | 2300 | ||
| cluster_9 | 72 | 2305 | ||
| cluster_8 | 56 | 846 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_7 | 1 | DCN | 4.19 | 4.867 | 1 |
| cluster_3 | 1 | C1QB | 3.5948 | 3.9174 | 0.9873 |
| cluster_10 | 1 | RNASE1 | 3.1402 | 3.4638 | 0.9875 |
| cluster_4 | 1 | PLA2G2A | 3.0518 | 3.4099 | 0.9461 |
| cluster_9 | 1 | IGFBP7 | 2.9018 | 3.6514 | 1 |
| cluster_5 | 1 | S100A8 | 2.7216 | 3.0485 | 0.8847 |
| cluster_6 | 1 | HLA-DRA | 2.3158 | 3.1882 | 0.9119 |
| cluster_8 | 1 | CD74 | 2.0647 | 4.0639 | 1 |
| cluster_2 | 1 | CTSW | 1.3448 | 1.4397 | 0.881 |
| cluster_1 | 1 | IL7R | 1.2247 | 1.3203 | 0.8248 |
| cluster_7 | 2 | MGP | 4.1717 | 4.8371 | 1 |
| cluster_3 | 2 | C1QC | 3.2867 | 3.5624 | 1 |
| cluster_4 | 2 | DCN | 2.9855 | 3.728 | 0.9419 |
| cluster_5 | 2 | S100A9 | 2.6748 | 3.0469 | 0.8678 |
| cluster_10 | 2 | C1QB | 2.6393 | 2.9984 | 0.9875 |
| cluster_9 | 2 | SPARC | 2.6234 | 3.384 | 1 |
| cluster_6 | 2 | CD74 | 2.0689 | 3.8559 | 0.954 |
| cluster_8 | 2 | HLA-DRA | 1.8404 | 2.9635 | 1 |
| cluster_2 | 2 | GZMA | 1.2822 | 1.3564 | 0.8539 |
| cluster_1 | 2 | LTB | 1.2049 | 1.3573 | 0.8162 |
| cluster_7 | 3 | LUM | 3.5107 | 3.9351 | 1 |
| cluster_3 | 3 | C1QA | 3.2778 | 3.5775 | 1 |
| cluster_4 | 3 | EFEMP1 | 2.7276 | 3.1899 | 0.9751 |
| cluster_9 | 3 | COL3A1 | 2.6009 | 3.2903 | 0.9306 |
| cluster_10 | 3 | C1QC | 2.5308 | 2.835 | 0.9875 |
| cluster_6 | 3 | HLA-DRB1 | 1.9229 | 2.7609 | 0.9272 |
| cluster_5 | 3 | LYZ | 1.6615 | 2.1519 | 0.8 |
| cluster_8 | 3 | MS4A1 | 1.4809 | 1.4901 | 0.9286 |
| cluster_2 | 3 | GNLY | 1.2604 | 1.2919 | 0.4739 |
| cluster_1 | 3 | CD3E | 1.1381 | 1.4169 | 0.9231 |
| cluster_7 | 4 | C7 | 3.3742 | 3.5135 | 0.9901 |
| cluster_3 | 4 | HLA-DRA | 2.9371 | 3.9957 | 0.9747 |
| cluster_4 | 4 | CCDC80 | 2.6553 | 3.1099 | 0.9793 |
| cluster_9 | 4 | COL1A2 | 2.5947 | 3.3645 | 0.9722 |
| cluster_10 | 4 | F13A1 | 2.48 | 2.5727 | 0.9625 |
| cluster_6 | 4 | HLA-DPA1 | 1.8531 | 2.511 | 0.8851 |
| cluster_8 | 4 | HLA-DQA1 | 1.3983 | 1.8044 | 0.9821 |
| cluster_5 | 4 | S100A12 | 1.0861 | 1.137 | 0.7051 |
| cluster_2 | 4 | PTPRC | 1.0334 | 1.8128 | 0.9708 |
| cluster_1 | 4 | CD69 | 1.0202 | 1.4892 | 0.8419 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
iCCA-066-04-1A
Sample ID
iCCA-066-04-1A
Dataset
CancerSCEM 2.0
Cohort
CancerSCEM 2.0 Chinese subset; Intrahepatic Cholangiocarcinoma
Age / Age Group
Pan-cancer Chinese cohort, per-donor ages not in CancerSCEM metadata
Sex
Not reported in public CancerSCEM metadata
Health Status
Intrahepatic Cholangiocarcinoma; Tumour
Tissue / Cell Source
Tumour
Modality
scRNA-seq (10X Genomics)
Cell Count
3,625
Analysis Status
Matrix available; UMAP generated by fallback sampled pipeline
UMAP Status
Ready
Metadata / Source Notes
Project ID: iCCA-066; Cancer type: Intrahepatic Cholangiocarcinoma; Source: NCBI (GEO); Accession: GSE201425; Country: CHN; Sample type: Tumour; Protocol: 10X Genomics; Matrix: iCCA-066-04-1A.counts.matrix.tsv.gz (6.72 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
Intrahepatic Cholangiocarcinoma
cancer type short
iCCA
library count
1
library sample ids
iCCA-066-04-1A
source reference
CancerSCEM 2.0 metadata table; data source=NCBI (GEO); accession=GSE201425; downloaded 2026-07-06
data accession
GSE201425
project id
iCCA-066
sample type
Tumour
country
CHN
data source
NCBI (GEO)
accession no
GSE201425
construction protocol
10X Genomics
transcriptome profile
Yes
metabolic profile
Yes
matrix status
Matrix incomplete; redownload required
matrix file name
iCCA-066-04-1A.counts.matrix.tsv.gz
matrix file size bytes
7044867
matrix file size mb
6.72
umap coordinates url
umap summary url
umap pipeline
Fallback Python normalize_total/log1p/HVG/SVD/UMAP; sampled 3000/3625 cells; generated 2026-07-09
matrix integrity status
Gzip EOF/truncated during UMAP generation