scAtria single-cell spatial atlas resource

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4 Datasets
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Examples Study ID HNSCC_41616773 Modality Spatial transcriptomics Technique Xenium Organ breast Disease state primary cancer Disease detail breast cancer
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Search: lymph node colonization × 4 matches 4 curated
PCF / CODEX / PhenoCycler Fusion Spatial proteomics Curated

HNSCC_41616773 PCF healthy lymph node cohort

Dataset key: HNSCCHealthyLN_41616773__PCF_CODEX

Lymphoid tissue 51

Disease detail: Healthy/control: Organ-specific lymph-node control/no cancer

Healthy/control 51
Samples
51
Cells
1,238,209
Curation
Curated
DEG
NA
Spatial
50/51
Open dataset
Other ST Spatial transcriptomics Curated

HNSCC_41616773 · Other ST

Dataset key: HNSCC_41616773__Other_ST

Lymph node metastasis 46/137 Lymphoid tissue 91/137

Disease detail: Primary cancer: Head and neck squamous cell carcinoma, Metastatic cancer: Lymphoid tissue metastasis from Oral cavity, Healthy/control: Organ-specific lymph-node control/no cancer

Primary cancer 73/137 Metastatic cancer 46/137 Healthy/control 18/137
Samples
137
Cells
1,156,046
Curation
Curated
DEG
Held
Spatial
137/137
Open dataset
PCF / CODEX / PhenoCycler Fusion Spatial proteomics Curated

HNSCC_41616773 PCF discovery cohort

Dataset key: HNSCCDiscovery_41616773__PCF_CODEX

Head and neck 189/390 Lymph node metastasis 138/390 Lymphoid tissue 63/390

Disease detail: Primary cancer: Head and neck squamous cell carcinoma, Metastatic cancer: Lymphoid tissue metastasis from Oral cavity, Healthy/control: Organ-specific lymph-node control/no cancer

Primary cancer 189/390 Metastatic cancer 138/390 Healthy/control 63/390
Samples
390
Cells
1,556,569
Curation
Curated
DEG
NA
Spatial
390/390
Open dataset
PCF / CODEX / PhenoCycler Fusion Spatial proteomics Curated

HNSCC_41616773 PCF validation cohort

Dataset key: HNSCCValidation_41616773__PCF_CODEX

Head and neck 11/34 Lymph node metastasis 10/34 Lymphoid tissue 13/34

Disease detail: Primary cancer: Head and neck squamous cell carcinoma, Metastatic cancer: Lymphoid tissue metastasis from Oral cavity, Healthy/control: Organ-specific lymph-node control/no cancer

Primary cancer 15/34 Metastatic cancer 10/34 Healthy/control 9/34
Samples
34
Cells
745,842
Curation
Curated
DEG
NA
Spatial
34/34
Open dataset