scAtria single-cell spatial atlas resource

Browse

? Browse is the search page: type a query, then refine by organ, technique, modality, curation, and dataset/sample view.
Dataset Sample
Card Table
94 Datasets
Search
Examples Study ID HNSCC_41616773 Modality Spatial transcriptomics Technique Xenium Organ breast Disease state primary cancer Disease detail breast cancer
Filter scope 94 matches · dataset view
Columns 8
Dataset table columns Selections persist in the URL and manifest download.
Reset columns
All records 94 matches 80 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
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
CosMx SMI / NanoString SMI Spatial transcriptomics Curated

IBD_42049732 · CosMx SMI / NanoString SMI

Dataset key: IBD_42049732__CosMx_SMI

Large intestine 34

Disease detail: Non-cancer disease: Inflammatory bowel disease

Non-cancer disease 34
Samples
34
Cells
43,034
Curation
Curated
DEG
NA
Spatial
34/34
Open dataset
MERFISH / MERSCOPE Spatial transcriptomics Curated

Intestine_39843748 · MERFISH / MERSCOPE

Dataset key: Intestine_39843748__MERFISH

Large intestine 2

Disease detail: Healthy/control: Healthy intestine

Healthy/control 2
Samples
2
Cells
470,081
Curation
Curated
DEG
NA
Spatial
0/2
Open dataset
Xenium Spatial transcriptomics Curated

Intestine_39843748 · Xenium

Dataset key: Intestine_39843748__Xenium

Large intestine 16

Disease detail: Healthy/control: Healthy intestine

Healthy/control 16
Samples
16
Cells
2,814,759
Curation
Curated
DEG
NA
Spatial
0/16
Open dataset
IMC / Imaging Mass Cytometry Spatial proteomics Curated

LUAD_36725934 · IMC / Imaging Mass Cytometry

Dataset key: LUAD_36725934__IMC

Lung 416

Disease detail: Primary cancer: Lung adenocarcinoma

Primary cancer 416
Samples
416
Cells
1,635,722
Curation
Curated
DEG
NA
Spatial
415/416
Open dataset
CosMx SMI / NanoString SMI Spatial transcriptomics Curated

LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI

Dataset key: HCC_41723121__CosMx_SMI

Liver 9

Disease detail: Primary cancer: Hepatocellular carcinoma

Primary cancer 9
Samples
9
Cells
1,446,124
Curation
Curated
DEG
NA
Spatial
0/9
Open dataset
CosMx SMI / NanoString SMI Spatial transcriptomics Curated

LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI

Dataset key: ICC_41723121__CosMx_SMI

Liver 6

Disease detail: Primary cancer: Intrahepatic cholangiocarcinoma

Primary cancer 6
Samples
6
Cells
901,465
Curation
Curated
DEG
NA
Spatial
0/6
Open dataset
MERFISH / MERSCOPE Spatial transcriptomics Curated

MERFISH 960-plex Vizgen showcase

Dataset key: MERFISH_960_Vizgen__MERFISH

Brain 3

Disease detail: Non-cancer disease: Alzheimer's disease, Healthy/control: Normal brain cortex

Non-cancer disease 2/3 Healthy/control 1/3
Samples
3
Cells
394,181
Curation
Curated
DEG
NA
Spatial
0/3
Open dataset