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HNSCC-127-03-1A

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 HNSCC-127-03-1A, generated 2026-07-09 12:54:49 +0800.

1,119Cells analyzed
29Clusters
19,730Expressed genes
2743Mean UMI
1074Mean genes
1.769Mean 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
Myeloid_APC 29 0.3443 1.5833 9
Fibroblast_stroma 29 0.2548 1.9764 8
T_NK_cytotoxic 29 0.1095 0.7407 10
B_plasma 29 0.1016 0.5341 7
Epithelial_tumor 29 0.078 0.9575 7
Endothelial 29 0.0706 0.761 7
Checkpoint_exhaustion 29 0.0685 0.2677 8
Proliferation 29 0.059 0.5482 7
Cluster QC
Cluster Cells Mean UMI Median Genes Mean Mito %
cluster_1 210 5063.2905 1434 2.7332
cluster_2 131 1996.4656 637 0.2826
cluster_3 124 1528.5968 526.5 0.8056
cluster_4 61 1964.4262 540 0.8286
cluster_5 60 1713.8167 567.5 0.8719
cluster_6 51 2329.0588 801 1.9985
cluster_7 40 1390.4 598 1.2723
cluster_8 40 2276.125 642.5 0.2795
cluster_9 35 2119.9714 809 1.6267
cluster_10 34 2015 778 1.4402
cluster_11 31 1804.9032 574 2.0928
cluster_12 30 1351.7667 796 3.5769
cluster_13 28 1908.4286 724 1.938
cluster_14 27 6577.4074 1965 4.8466
cluster_15 25 879.2 316 0.4683
cluster_16 23 2375.2174 1096 4.127
cluster_17 21 6920.8095 2118 3.8393
cluster_18 21 1666.2857 512 1.4651
cluster_19 17 3617 1470 2.5386
cluster_20 13 2526.2308 397 1.6375
cluster_21 13 1147.3846 654 0.5529
cluster_22 12 1378 737.5 1.9259
cluster_23 11 1848 973 4.9438
cluster_24 11 5257.6364 2347 4.1002
Top Cluster Marker Genes
Cluster Rank Gene Score Mean Expr Detect Fraction
cluster_20 1 HBB 5.3974 5.6741 1
cluster_27 1 SPP1 4.552 4.7274 1
cluster_24 1 MMP9 3.6258 3.8097 1
cluster_15 1 S100A8 3.5512 4.4145 1
cluster_26 1 TET2 3.3661 3.6661 1
cluster_8 1 KRT14 3.3382 3.7743 1
cluster_17 1 LYZ 3.1697 3.3605 0.9524
cluster_14 1 COL3A1 3.1362 3.3806 1
cluster_16 1 ENPP1 3.0926 3.1515 1
cluster_4 1 CXCL8 2.9885 3.6811 1
cluster_9 1 TPSB2 2.9542 2.9635 1
cluster_19 1 FLT1 2.8579 2.9077 1
cluster_29 1 ANGPT2 2.8428 2.905 1
cluster_22 1 IGKC 2.673 2.6794 1
cluster_2 1 KRT14 2.5918 2.8439 0.9924
cluster_5 1 FTL 2.4875 4.0636 1
cluster_10 1 CST3 2.3856 2.8432 0.9706
cluster_3 1 S100A8 2.1516 2.8557 0.9355
cluster_11 1 TIMP1 2.105 2.3144 0.9355
cluster_23 1 LYZ 2.0833 2.3132 1
cluster_7 1 IGFBP7 1.9504 2.1825 1
cluster_25 1 IL7R 1.886 2.0799 1
cluster_1 1 CCL5 1.7459 1.8498 0.719
cluster_28 1 HIST1H4C 1.7428 1.8964 0.9
cluster_21 1 SAMSN1 1.3874 2.0867 1
cluster_18 1 GNG11 1.3412 1.3789 0.8571
cluster_6 1 IL32 1.3034 1.7048 0.902
cluster_13 1 IKZF2 1.1565 1.2303 0.8929
cluster_12 1 RAB11A 0.7465 1.1988 0.7333
cluster_20 2 HBA2 4.4753 4.7133 1
cluster_15 2 S100A9 3.4252 4.4709 1
cluster_24 2 EXT1 3.2759 3.5603 1
cluster_26 2 KYNU 3.2043 3.3812 1
cluster_14 2 COL1A2 3.1174 3.5287 1
cluster_27 2 RNASE1 3.1151 3.17 1
cluster_8 2 KRT16 2.9655 3.0319 1
cluster_19 2 INSR 2.7098 2.7306 1
cluster_29 2 ZBTB44 2.6384 2.7151 1
cluster_9 2 CPA3 2.5417 2.5459 1
cluster_17 2 CXCL8 2.5311 3.3392 1

Primary Metadata

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

Donor ID
HNSCC-127-03-1A
Sample ID
HNSCC-127-03-1A
Dataset
CancerSCEM 2.0
Cohort
CancerSCEM 2.0 Chinese subset; Head and Neck 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
Head and Neck Squamous Cell Carcinoma; Tumour
Tissue / Cell Source
Tumour
Modality
scRNA-seq (10X Genomics)
Cell Count
1,119
Analysis Status
Matrix available; UMAP generated
UMAP Status
Ready
Metadata / Source Notes
Project ID: HNSCC-127; Cancer type: Head and Neck Squamous Cell Carcinoma; Source: NCBI (GEO); Accession: GSE185965; Country: CHN; Sample type: Tumour; Protocol: 10X Genomics; Matrix: HNSCC-127-03-1A.counts.matrix.tsv.gz (1.95 MB); UMAP: Scanpy-generated donor-level UMAP preview; cells=1119; raw genes=19872; Leiden clusters=29; 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
Head and Neck Squamous Cell Carcinoma
cancer type short
HNSCC
library count
1
library sample ids
HNSCC-127-03-1A
source reference
CancerSCEM 2.0 metadata table; data source=NCBI (GEO); accession=GSE185965; downloaded 2026-07-06
data accession
GSE185965
project id
HNSCC-127
sample type
Tumour
country
CHN
data source
NCBI (GEO)
accession no
GSE185965
construction protocol
10X Genomics
transcriptome profile
Yes
metabolic profile
Yes
matrix status
Matrix available
matrix file name
HNSCC-127-03-1A.counts.matrix.tsv.gz
matrix file size bytes
2049485
matrix file size mb
1.95
matrix download url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_matrix/HNSCC-127-03-1A.counts.matrix.tsv.gz
umap coordinates url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_umap/HNSCC-127-03-1A.umap.tsv.gz
umap summary url
http://8.142.154.29/LACA/data/human_immune_atlas/cancerscem_2_umap/HNSCC-127-03-1A.summary.json
umap pipeline
Scanpy 1.9.8 normalize_total/log1p/HVG/PCA/neighbors/leiden/umap; cells=1119; raw_genes=19872; leiden_clusters=29; generated 2026-07-07
matrix integrity status
Gzip readable; UMAP generated