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ESCC-111-41-1A

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 ESCC-111-41-1A, generated 2026-07-09 12:54:49 +0800.

2,000Cells analyzed
19Clusters
22,684Expressed genes
6729Mean UMI
1890Mean genes
3.07Mean 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
T_NK_cytotoxic 19 0.567 1.9039 10
B_plasma 19 0.5601 2.6042 8
Myeloid_APC 19 0.3195 1.8395 9
Fibroblast_stroma 19 0.2636 3.0501 8
Checkpoint_exhaustion 19 0.228 0.9531 8
Proliferation 19 0.1757 1.7226 7
Endothelial 19 0.1094 1.144 7
Epithelial_tumor 19 0.0791 0.9772 8
Cluster QC
Cluster Cells Mean UMI Median Genes Mean Mito %
cluster_1 442 5545.3077 1772.5 2.9733
cluster_2 240 4662.9083 1787 3.6972
cluster_3 206 4472.9126 1589.5 3.1995
cluster_4 195 5399.0103 910 1.5049
cluster_5 147 9721.4286 2044 2.7367
cluster_6 130 12679.4077 3307 3.8362
cluster_7 97 3831.4948 1500 3.2062
cluster_8 85 5956.4588 1652 3.766
cluster_10 66 4881.2424 1805.5 3.3887
cluster_9 66 23321.8485 2123.5 1.8679
cluster_11 65 6294.8308 2015 3.382
cluster_12 61 9946.3279 2077 2.7064
cluster_13 47 893.7872 313 1.0721
cluster_14 40 4490 1312.5 4.3498
cluster_15 36 4386.8611 1895 6.0217
cluster_16 32 12111.2812 3516 3.2414
cluster_17 26 1495.6154 703.5 4.3541
cluster_18 10 7879.4 2383.5 5.4146
cluster_19 9 21826.3333 1424 1.1722
Top Cluster Marker Genes
Cluster Rank Gene Score Mean Expr Detect Fraction
cluster_19 1 IGKV3-20 8.671 8.7547 1
cluster_6 1 COL1A1 4.6013 4.6315 0.9923
cluster_18 1 IGFBP7 4.2665 4.565 1
cluster_9 1 IGHG1 3.9318 4.0356 0.8182
cluster_12 1 IL1B 3.2006 3.3187 0.9016
cluster_14 1 TPSAB1 3.1903 3.1931 0.975
cluster_15 1 IGFBP7 3.0339 3.2991 1
cluster_5 1 HLA-DRA 2.8274 3.4888 0.9864
cluster_16 1 STMN1 2.7534 3.0762 1
cluster_8 1 CD74 2.636 4.6401 1
cluster_4 1 S100A9 2.5058 2.7894 0.8308
cluster_11 1 GNLY 2.3542 3.0041 0.8
cluster_13 1 CXCL8 2.3072 2.5605 0.9149
cluster_2 1 GZMA 2.2918 2.9332 0.9583
cluster_10 1 GZMA 2.285 3.1261 0.9848
cluster_7 1 NKG7 2.1077 2.9475 1
cluster_1 1 IL32 1.7522 2.8287 0.9819
cluster_3 1 CCL5 1.7197 2.5387 0.9369
cluster_17 1 Z93241.1 0.5483 0.5867 0.4231
cluster_19 2 AC233755.2 6.1807 6.2147 1
cluster_6 2 SPARC 4.1965 4.2638 0.9923
cluster_18 2 SPARC 3.5199 3.8423 1
cluster_9 2 IGKC 3.4511 3.6175 0.8636
cluster_12 2 IFI30 2.9683 3.4023 0.9836
cluster_14 2 CPA3 2.8127 2.8151 0.9
cluster_5 2 CD74 2.7637 4.6767 0.9932
cluster_16 2 TUBA1B 2.7037 3.6673 1
cluster_8 2 HLA-DRA 2.5373 3.2987 1
cluster_4 2 S100A7 2.5037 2.5603 0.7128
cluster_2 2 GNLY 2.0571 2.5366 0.8542
cluster_13 2 G0S2 1.8583 2.0759 0.8723
cluster_15 2 IFITM3 1.794 2.7764 1
cluster_7 2 CCL5 1.7665 2.677 0.9897
cluster_10 2 CCL5 1.7365 2.6754 0.9394
cluster_11 2 CD7 1.554 2.6647 0.9385
cluster_1 2 S100A4 1.3081 2.4858 0.9208
cluster_3 2 NKG7 1.2888 2.0981 0.9078
cluster_17 2 SERPINB9 0.4126 0.9194 0.7308
cluster_19 3 IGKC 5.9241 6.1777 1
cluster_6 3 COL1A2 4.0915 4.1129 0.9923

Primary Metadata

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

Donor ID
ESCC-111-41-1A
Sample ID
ESCC-111-41-1A
Dataset
CancerSCEM 2.0
Cohort
CancerSCEM 2.0 Chinese subset; Esophageal Squamous Cell Carcinoma
Age / Age Group
Pan-cancer Chinese cohort, per-donor ages not in CancerSCEM metadata
Sex
Not reported in public CancerSCEM metadata
Health Status
Esophageal Squamous Cell Carcinoma; Tumour
Tissue / Cell Source
Tumour
Modality
scRNA-seq (10X Genomics)
Cell Count
3,682
Analysis Status
Matrix available; UMAP generated
UMAP Status
Ready
Metadata / Source Notes
Project ID: ESCC-111; Cancer type: Esophageal Squamous Cell Carcinoma; Source: NCBI (GEO); Accession: GSE160269; Country: CHN; Sample type: Tumour; Protocol: 10X Genomics; Matrix: ESCC-111-41-1A.counts.matrix.tsv.gz (8.42 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=3682; raw genes=23912; Leiden clusters=19; 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
Esophageal Squamous Cell Carcinoma
cancer type short
ESCC
library count
1
library sample ids
ESCC-111-41-1A
source reference
CancerSCEM 2.0 metadata table; data source=NCBI (GEO); accession=GSE160269; downloaded 2026-07-06
data accession
GSE160269
project id
ESCC-111
sample type
Tumour
country
CHN
data source
NCBI (GEO)
accession no
GSE160269
construction protocol
10X Genomics
transcriptome profile
Yes
metabolic profile
Yes
matrix status
Matrix available
matrix file name
ESCC-111-41-1A.counts.matrix.tsv.gz
matrix file size bytes
8832172
matrix file size mb
8.42
matrix download url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_matrix/ESCC-111-41-1A.counts.matrix.tsv.gz
umap coordinates url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_umap/ESCC-111-41-1A.umap.tsv.gz
umap summary url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_umap/ESCC-111-41-1A.summary.json
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=3682; raw_genes=23912; leiden_clusters=19; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated