scAtria single-cell spatial atlas resource

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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: HNSCCHealthyLN_41616773 × 35 matches 32 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
10/51
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
112/137
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
13/34
Open dataset
MIBI-TOF / Multiplexed Ion Beam Imaging Spatial proteomics Curated

BRCA_35063072 · MIBI-TOF / Multiplexed Ion Beam Imaging

Dataset key: BRCA_35063072__MIBI_TOF

Breast 79

Disease detail: Primary cancer: Breast cancer (ductal carcinoma in situ), Healthy/control: Normal/healthy breast tissue control

Primary cancer 70/79 Healthy/control 9/79
Samples
79
Cells
69,672
Curation
Curated
DEG
Available
Spatial
79/79
Open dataset
PCF / CODEX / PhenoCycler Fusion Spatial proteomics Curated

BoneMarrow_38714197 · PCF / CODEX / PhenoCycler Fusion

Dataset key: BoneMarrow_38714197__PCF_CODEX

Bone marrow 32

Disease detail: Healthy/control: Normal/healthy bone marrow control, Primary cancer: Acute myeloid leukemia

Healthy/control 27/32 Primary cancer 5/32
Samples
32
Cells
1,214,574
Curation
Curated
DEG
Caveat
Spatial
13/32
Open dataset
CosMx SMI / NanoString SMI Spatial transcriptomics Curated

Bruker CosMx 1k FFPE showcase

Dataset key: CosMx1k_Bruker__CosMx_SMI

Liver 2

Disease detail: Healthy/control: Normal/healthy liver control, Primary cancer: Hepatocellular carcinoma

Healthy/control 1/2 Primary cancer 1/2
Samples
2
Cells
793,318
Curation
Curated
DEG
NA
Spatial
0/2
Open dataset
CosMx SMI Protein Spatial proteomics Curated

Bruker CosMx 64-protein FFPE showcase

Dataset key: CosMx64_Bruker__CosMx_SMI_protein

Breast 1/2 Lymphoid tissue 1/2

Disease detail: Healthy/control: Normal/healthy breast tissue control

Healthy/control 2
Samples
2
Cells
1,398,757
Curation
Curated
DEG
NA
Spatial
0/2
Open dataset