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iCCA-066-03-1A

De-identified Human Immune Atlas donor/sample detail for CancerSCEM 2.0. The record preserves available public metadata while avoiding direct identifiers.

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Donor-Level Analysis Results

Matrix-backed CancerSCEM donor analysis for iCCA-066-03-1A, generated 2026-07-09 12:54:49 +0800.

1,999Cells analyzed
21Clusters
22,364Expressed genes
6917Mean UMI
2177Mean genes
2.388Mean mito %
Donor-level analysis panel
Cluster cell counts, cluster-by-program score heatmap, and top marker genes.
CancerSCEM Deep Analysis Donor JSON UMAP Coordinates UMAP Summary
Gene Program Summary
Program Clusters Mean Score Max Score Genes Used
Fibroblast_stroma 21 0.4473 3.087 8
Epithelial_tumor 21 0.3331 1.3443 8
B_plasma 21 0.3061 1.4813 8
T_NK_cytotoxic 21 0.2309 1.3218 10
Myeloid_APC 21 0.1779 1.6696 9
Proliferation 21 0.1569 1.1696 7
Endothelial 21 0.1547 1.3304 7
Checkpoint_exhaustion 21 0.0664 0.3861 8
Cluster QC
Cluster Cells Mean UMI Median Genes Mean Mito %
cluster_1 234 2686.4872 1183 1.7089
cluster_2 227 11883.8106 3331 2.3769
cluster_3 218 9612.9358 3097 4.6097
cluster_4 212 8586.1934 2565.5 3.5519
cluster_5 205 2712 1146 1.75
cluster_6 157 8237.1083 2258 1.6927
cluster_7 120 2490.8833 1038 2.1602
cluster_8 91 5383.1978 2053 2.3348
cluster_9 87 3962.4598 1594 1.732
cluster_10 72 11852.6806 3196 1.3514
cluster_11 65 10580.5077 3431 3.4278
cluster_12 59 8307.1017 2619 1.7417
cluster_13 51 3241.9608 1363 1.6658
cluster_14 48 3397.6875 1453.5 1.448
cluster_15 46 8968.2826 3132 2.9612
cluster_16 29 6551.7586 579 0.9143
cluster_17 25 17051.44 3408 0.6181
cluster_18 19 2603.6842 516 0.9103
cluster_19 17 6042.2941 2472 1.5772
cluster_20 10 2830.3 1259 1.3153
cluster_21 7 4618.1429 1836 2.3324
Top Cluster Marker Genes
Cluster Rank Gene Score Mean Expr Detect Fraction
cluster_19 1 CCL21 5.2301 5.2571 1
cluster_17 1 TIMP1 4.0297 5.0885 1
cluster_10 1 COL1A2 3.9944 4.1344 1
cluster_12 1 MGP 3.6262 3.8558 0.9831
cluster_15 1 SPP1 3.5364 4.695 1
cluster_21 1 TPSAB1 3.2623 3.2623 1
cluster_6 1 IFI30 3.1361 3.326 0.9873
cluster_14 1 NKG7 2.6152 2.959 1
cluster_2 1 S100A6 2.5793 4.8301 0.9956
cluster_3 1 DEFB1 2.5328 3.5887 0.9817
cluster_7 1 CD74 2.4708 3.9573 1
cluster_16 1 IGKC 2.4565 2.4812 0.6207
cluster_9 1 CCL5 2.4083 2.9038 0.9885
cluster_4 1 DEFB1 2.1818 3.2825 0.9292
cluster_8 1 RNASE1 2.1655 2.2844 0.967
cluster_20 1 FXYD5 1.913 2.8749 1
cluster_1 1 CCL5 1.8298 2.216 0.9786
cluster_11 1 TUBA1B 1.7012 2.7351 0.9538
cluster_18 1 FTL 1.6666 4.3265 1
cluster_13 1 IL32 1.1442 2.0379 0.9804
cluster_5 1 IL7R 0.9178 1.0239 0.7122
cluster_17 2 COL1A2 3.7966 4.0329 1
cluster_10 2 COL1A1 3.7768 4.0815 0.9722
cluster_21 2 TPSB2 3.2083 3.2087 1
cluster_12 2 IGFBP7 3.042 4.2669 1
cluster_6 2 CD74 2.9604 4.3626 0.9936
cluster_19 2 FABP5 2.7896 3.0489 1
cluster_15 2 APCS 2.6338 3.042 0.9783
cluster_16 2 IGHG1 2.384 2.398 0.6897
cluster_9 2 NKG7 2.34 2.6447 1
cluster_14 2 GNLY 2.304 2.5155 0.8958
cluster_8 2 VWF 2.1444 2.1567 0.9011
cluster_2 2 KRT19 2.122 2.6362 0.9736
cluster_7 2 HLA-DRA 2.075 2.5807 0.9917
cluster_3 2 FXYD2 2.0722 2.7772 0.9862
cluster_4 2 SPP1 1.8368 2.882 0.8679
cluster_11 2 STMN1 1.5894 2.0349 0.9692
cluster_20 2 IL7R 1.45 1.643 1
cluster_18 2 HLA-DRA 1.435 2.0516 0.7895
cluster_1 2 CCL4 1.2133 1.5757 0.7265

Primary Metadata

Core de-identified metadata fields migrated from the ImmuneAging donor manifest.

Donor ID
iCCA-066-03-1A
Sample ID
iCCA-066-03-1A
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
3,981
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: Tumour; Protocol: 10X Genomics; Matrix: iCCA-066-03-1A.counts.matrix.tsv.gz (9.97 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=3981; raw genes=22831; 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
Intrahepatic Cholangiocarcinoma
cancer type short
iCCA
library count
1
library sample ids
iCCA-066-03-1A
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 available
matrix file name
iCCA-066-03-1A.counts.matrix.tsv.gz
matrix file size bytes
10450975
matrix file size mb
9.97
matrix download url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_matrix/iCCA-066-03-1A.counts.matrix.tsv.gz
umap coordinates url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_umap/iCCA-066-03-1A.umap.tsv.gz
umap summary url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_umap/iCCA-066-03-1A.summary.json
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=3981; raw_genes=22831; leiden_clusters=21; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated