iCCA-066-02-1A
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 iCCA-066-02-1A, generated 2026-07-09 12:54:49 +0800.
2,000Cells analyzed
17Clusters
17,461Expressed genes
4243Mean UMI
1478Mean genes
2.229Mean mito %
Gene Program Summary
| Program | Clusters | Mean Score | Max Score | Genes Used |
|---|---|---|---|---|
| T_NK_cytotoxic | 17 | 0.7228 | 1.7163 | 10 |
| B_plasma | 17 | 0.4858 | 2.5163 | 8 |
| Myeloid_APC | 17 | 0.4306 | 1.7081 | 9 |
| Proliferation | 17 | 0.1052 | 1.0226 | 7 |
| Checkpoint_exhaustion | 17 | 0.0638 | 0.2311 | 8 |
| Endothelial | 17 | 0.0602 | 0.3119 | 5 |
| Fibroblast_stroma | 17 | 0.0236 | 0.0961 | 2 |
| Epithelial_tumor | 17 | 0.0007 | 0.0045 | 3 |
Cluster QC
| Cluster | Cells | Mean UMI | Median Genes | Mean Mito % |
|---|---|---|---|---|
| cluster_1 | 411 | 3847.837 | 1401 | 2.0663 |
| cluster_2 | 298 | 3603.0738 | 1187.5 | 2.1266 |
| cluster_3 | 272 | 3691.511 | 1373 | 2.3837 |
| cluster_4 | 258 | 4148.6085 | 1393 | 2.4011 |
| cluster_5 | 185 | 4076.0378 | 1492 | 2.2563 |
| cluster_6 | 179 | 4472.8492 | 1517 | 1.9808 |
| cluster_7 | 103 | 3764.8932 | 1454 | 2.3892 |
| cluster_8 | 57 | 3364.1404 | 1417 | 2.468 |
| cluster_9 | 46 | 5846.0217 | 1981 | 2.506 |
| cluster_10 | 42 | 4556.4762 | 1505.5 | 2.4323 |
| cluster_11 | 32 | 4800.0312 | 1290.5 | 2.6252 |
| cluster_12 | 26 | 17384.0769 | 2857 | 1.9164 |
| cluster_13 | 25 | 9799.16 | 2711 | 2.0924 |
| cluster_15 | 25 | 3623.04 | 1435 | 2.2631 |
| cluster_14 | 25 | 3174.16 | 595 | 2.2523 |
| cluster_16 | 12 | 9976.9167 | 2665.5 | 1.836 |
| cluster_17 | 4 | 5164.75 | 1283 | 2.3297 |
Top Cluster Marker Genes
| Cluster | Rank | Gene | Score | Mean Expr | Detect Fraction |
|---|---|---|---|---|---|
| cluster_12 | 1 | JCHAIN | 4.9135 | 4.9246 | 1 |
| cluster_16 | 1 | HLA-DRA | 3.9291 | 4.6196 | 1 |
| cluster_1 | 1 | S100A8 | 3.6338 | 3.7229 | 0.983 |
| cluster_14 | 1 | PPBP | 3.1943 | 3.2842 | 1 |
| cluster_11 | 1 | CD74 | 2.8857 | 4.7169 | 1 |
| cluster_9 | 1 | LST1 | 2.8101 | 3.2335 | 1 |
| cluster_7 | 1 | GNLY | 2.8035 | 3.4226 | 0.9806 |
| cluster_8 | 1 | GNLY | 2.5034 | 3.1955 | 1 |
| cluster_15 | 1 | TRBV7-3 | 2.4659 | 2.4888 | 1 |
| cluster_13 | 1 | STMN1 | 2.4491 | 2.5705 | 1 |
| cluster_3 | 1 | NKG7 | 2.1185 | 2.9966 | 1 |
| cluster_5 | 1 | NKG7 | 2.0144 | 2.9943 | 0.9892 |
| cluster_10 | 1 | NKG7 | 1.9438 | 3.0693 | 1 |
| cluster_4 | 1 | IL7R | 1.3891 | 2.0409 | 0.9806 |
| cluster_17 | 1 | PF4 | 1.2506 | 1.3104 | 1 |
| cluster_6 | 1 | IL32 | 0.9058 | 2.4483 | 0.9888 |
| cluster_2 | 1 | LTB | 0.7584 | 1.3387 | 0.9094 |
| cluster_16 | 2 | CST3 | 3.785 | 4.3993 | 1 |
| cluster_12 | 2 | IGKC | 3.5126 | 3.5285 | 0.7308 |
| cluster_1 | 2 | S100A9 | 3.4211 | 3.5316 | 0.9878 |
| cluster_11 | 2 | HLA-DRA | 2.6829 | 3.354 | 1 |
| cluster_9 | 2 | IFI30 | 2.6185 | 3.2001 | 1 |
| cluster_7 | 2 | NKG7 | 2.5039 | 3.5412 | 0.9903 |
| cluster_8 | 2 | TRBV30 | 2.2754 | 2.3465 | 1 |
| cluster_15 | 2 | NKG7 | 2.1372 | 3.2768 | 1 |
| cluster_14 | 2 | PF4 | 2.1166 | 2.1525 | 1 |
| cluster_13 | 2 | HMGN2 | 2.1108 | 2.7678 | 0.96 |
| cluster_10 | 2 | CCL5 | 1.8892 | 2.9828 | 1 |
| cluster_3 | 2 | GZMH | 1.7785 | 2.2108 | 0.9963 |
| cluster_5 | 2 | CCL5 | 1.7292 | 2.7024 | 0.973 |
| cluster_17 | 2 | TRBV5-1 | 1.2177 | 1.301 | 0.5 |
| cluster_4 | 2 | LTB | 0.9891 | 1.5549 | 0.938 |
| cluster_6 | 2 | LDHB | 0.8452 | 1.882 | 0.9721 |
| cluster_2 | 2 | LDHB | 0.7511 | 1.7516 | 0.9765 |
| cluster_16 | 3 | CD74 | 3.7029 | 5.5581 | 1 |
| cluster_12 | 3 | MZB1 | 3.1513 | 3.1582 | 1 |
| cluster_1 | 3 | LYZ | 3.1208 | 3.2467 | 0.9951 |
| cluster_9 | 3 | AIF1 | 2.5694 | 3.0604 | 1 |
| cluster_8 | 3 | NKG7 | 2.0816 | 3.1886 | 1 |
| cluster_11 | 3 | MS4A1 | 2.0338 | 2.0522 | 1 |
Primary Metadata
Core de-identified metadata fields migrated from the ImmuneAging donor manifest.
Donor ID
iCCA-066-02-1A
Sample ID
iCCA-066-02-1A
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; PBMC
Tissue / Cell Source
PBMC
Modality
scRNA-seq (10X Genomics)
Cell Count
4,950
Analysis Status
Matrix available; UMAP generated
UMAP Status
Ready
Metadata / Source Notes
Project ID: iCCA-066; Cancer type: Intrahepatic Cholangiocarcinoma; Source: NCBI (GEO); Accession: GSE201425; Country: CHN; Sample type: PBMC; Protocol: 10X Genomics; Matrix: iCCA-066-02-1A.counts.matrix.tsv.gz (8.08 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=4950; raw genes=17885; 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
Intrahepatic Cholangiocarcinoma
cancer type short
iCCA
library count
1
library sample ids
iCCA-066-02-1A
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
PBMC
country
CHN
data source
NCBI (GEO)
accession no
GSE201425
construction protocol
10X Genomics
transcriptome profile
Yes
metabolic profile
Yes
matrix status
Matrix available
matrix file name
iCCA-066-02-1A.counts.matrix.tsv.gz
matrix file size bytes
8469195
matrix file size mb
8.08
matrix download url
umap coordinates url
umap summary url
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=4950; raw_genes=17885; leiden_clusters=17; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated