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
67 Datasets
SearchFiltered
Examples Study ID HNSCC_41616773 Modality Spatial transcriptomics Technique Xenium Organ breast Disease state primary cancer Disease detail breast cancer
Filter scope 67 matches · dataset view
Reset
Columns 8
Dataset table columns Selections persist in the URL and manifest download.
Reset columns
Search: breast cancer × 67 matches 59 curated
Dataset Organs ?For mixed datasets, fractions show sample counts per organ. Disease state Technique Samples Cells Spatial module Curation
Xenium Human Breast Gene Expression Panel 10x Genomics showcase
XeniumBreast_10xGenomics__Xenium
Breast 6
Primary cancer 6
Xenium 6 3,652,654
0/6
 Curated
Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase
XeniumBreastJanesick_10xGenomics__Xenium
Breast 12
Primary cancer 11/12 Healthy/control 1/12
Xenium 12 3,442,976
0/12
 Curated
10x Genomics Atera showcase
Atera_10xGenomics__Atera
Breast 1/2 Uterus/Cervix 1/2
Primary cancer 2
Atera 2 887,633
0/2
 Curated
10x Genomics Visium HD p2 TMA showcase
VisiumHD_p2_TMA__Visium_HD
Breast 36
Primary cancer 36
Visium HD 36 117,494
36/36
 Curated
10x Genomics Visium HD p2 TissueArray showcase
VisiumHD_p2_TissueArray__Visium_HD
Breast 1/3 Large intestine 1/3 Lung 1/3
Primary cancer 3
Visium HD 3 506,235
0/3
 Curated
10x Genomics Visium HD showcase
Visium_HD_10xGenomics__Visium_HD
Breast 3/24 Kidney 1/24 Large intestine 5/24 Lung 5/24 Lymphoid tissue 2/24 Ovary 5/24 Pancreas 2/24 Prostate 1/24
Primary cancer 20/24 Healthy/control 4/24
Visium HD 24 5,379,712
0/24
 Curated
10x Genomics Xenium Prime 5K showcase
Xenium5k_10xGenomics__Xenium
Breast 1/9 Lung 1/9 Lymphoid tissue 1/9 Ovary 3/9 Prostate 1/9 Skin 1/9 Uterus/Cervix 1/9
Primary cancer 8/9 Non-cancer disease 1/9
Xenium 9 4,598,042
0/9
 Curated
BRCA_31959985 · IMC / Imaging Mass Cytometry
BRCA_31959985__IMC
Breast 376/381 Liver 5/381
Primary cancer 289/381 Healthy/control 92/381
IMC 381 855,668
380/381
 Curated
BRCA_35063072 · MIBI-TOF / Multiplexed Ion Beam Imaging
BRCA_35063072__MIBI_TOF
Breast 79
Primary cancer 70/79 Healthy/control 9/79
MIBI 79 69,672
79/79
 Curated
BRCA_35122013 · IMC / Imaging Mass Cytometry
BRCA_35122013__IMC
Breast 548
Primary cancer 548
IMC 548 479,844
547/548
 Curated
Bruker CosMx WTx FFPE showcase
CosMxWTx_Bruker__CosMx_SMI
Brain 1/9 Breast 2/9 Kidney 1/9 Large intestine 1/9 Pancreas 3/9 Skin 1/9
Primary cancer 5/9 Healthy/control 4/9
CosMx 9 2,878,028
0/9
 Curated
MERFISH 500-plex Vizgen showcase
MERFISH_500_Vizgen__MERFISH
Breast 1/18 Large intestine 2/18 Liver 2/18 Lung 2/18 Ovary 4/18 Prostate 2/18 Skin 2/18 Uterus/Cervix 3/18
Primary cancer 18
MERFISH 18 10,196,835
0/18
 Curated
MERFISH 815-plex Vizgen showcase
MERFISH_815_Vizgen__MERFISH
Breast 5/6 Large intestine 1/6
Primary cancer 6
MERFISH 6 1,051,006
0/6
 Curated
TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion
TNBC_38194915__PCF_CODEX
Breast 27
Primary cancer 27
CODEX 27 2,597,738
0/27
 Curated
CervicalCancer_CmTSA_41807362
CervicalCancer_CmTSA_41807362__CmTSA
Uterus/Cervix 2
Primary cancer 2
CmTSA 2 1,564,537
0/2
 Curated
LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI
HCC_41723121__CosMx_SMI
Liver 9
Primary cancer 9
CosMx 9 1,446,124
0/9
 Curated
LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI
ICC_41723121__CosMx_SMI
Liver 6
Primary cancer 6
CosMx 6 901,465
0/6
 Curated
Xenium Human Multi-Tissue and Cancer Panel showcase
XeniumMulti_10xGenomics__Xenium
Bone marrow 2/20 Heart 1/20 Kidney 3/20 Liver 2/20 Lung 2/20 Lymphoid tissue 3/20 Musculoskeletal 1/20 Ovary 1/20 Pancreas 3/20 Skin 2/20
Healthy/control 9/20 Primary cancer 9/20 Non-cancer disease 2/20
Xenium 20 5,095,938
0/20
 Curated
10x Genomics Visium HD p2 WholeSlide showcase
VisiumHD_p2_WholeSlide__Visium_HD
Heart 1/3 Large intestine 2/3
Primary cancer 2/3 Healthy/control 1/3
Visium HD 3 1,729,339
0/3
 Curated
B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion
B-NHL_38379051__PCF_CODEX
Lymphoid tissue 35
Primary cancer 35
CODEX 35 5,690,284
0/35
 Curated
BoneMarrow_38714197 · PCF / CODEX / PhenoCycler Fusion
BoneMarrow_38714197__PCF_CODEX
Bone marrow 32
Healthy/control 27/32 Primary cancer 5/32
CODEX 32 1,214,574
13/32
 Curated
BrainTumor_36725935 · IMC / Imaging Mass Cytometry
BrainTumor_36725935__IMC
Brain 393
Primary cancer 270/393 Metastatic cancer 123/393
IMC 393 1,163,362
390/393
 Curated
Bruker CosMx 1k FFPE showcase
CosMx1k_Bruker__CosMx_SMI
Liver 2
Healthy/control 1/2 Primary cancer 1/2
CosMx 2 793,318
0/2
 Curated
CML_41592325 · PCF / CODEX / PhenoCycler Fusion
CML_41592325__PCF_CODEX
Bone marrow 55
Primary cancer 55
CODEX 55 2,033,725
0/55
 Curated
CRC_32763154 · PCF / CODEX / PhenoCycler Fusion
CRC_32763154__PCF_CODEX
Large intestine 140
Primary cancer 140
CODEX 140 258,385
140/140
 Curated
CRC_40189697 · IMC / Imaging Mass Cytometry
CRC_40189697__IMC
Large intestine 170
Primary cancer 170
IMC 170 903,125
170/170
 Curated
CRC_41986711 · CosMx SMI / NanoString SMI
CRC_41986711__CosMx_SMI
Large intestine 352
Primary cancer 352
CosMx 352 629,446
350/352
 Curated
DLBCL_41874448 · CosMx SMI / NanoString SMI
DLBCL_41874448__CosMx_SMI
Lymphoid tissue 56
Primary cancer 56
CosMx 56 182,646
56/56
 Curated
DLBCL_41874448 · PCF / CODEX / PhenoCycler Fusion
DLBCL_41874448__PCF_CODEX
Lymphoid tissue 30
Primary cancer 30
CODEX 30 1,172,666
2/30
 Curated
HCC_39304772 · PCF / CODEX / PhenoCycler Fusion
HCC_39304772__PCF_CODEX
Liver 124
Primary cancer 124
CODEX 124 1,065,284
101/124
 Curated
HCC_39327501 · PCF / CODEX / PhenoCycler Fusion
HCC_39327501__PCF_CODEX
Liver 288
Primary cancer 288
CODEX 288 3,231,437
230/288
 Curated
HCC_39455893 · IMC / Imaging Mass Cytometry
HCC_39455893__IMC
Liver 38
Primary cancer 38
IMC 38 61,393
38/38
 Curated
HCC_39965889 · PCF / CODEX / PhenoCycler Fusion
HCC_39965889__PCF_CODEX
Liver 31
Primary cancer 31
CODEX 31 387,155
19/31
 Curated
HGSC_39179931 · CosMx SMI / NanoString SMI
HGSC_39179931__CosMx_SMI
Ovary 166
Primary cancer 166
CosMx 166 1,724,825
162/166
 Curated
HGSC_39179931 · MERFISH / MERSCOPE
HGSC_39179931__MERFISH
Ovary 4
Primary cancer 4
MERFISH 4 425,578
1/4
 Curated
HGSC_39179931 · Xenium
HGSC_39179931__Xenium
Ovary 32
Primary cancer 32
Xenium 32 447,874
18/32
 Curated
HNSCC_41616773 · Other ST
HNSCC_41616773__Other_ST
Lymph node metastasis 46/137 Lymphoid tissue 91/137
Primary cancer 73/137 Metastatic cancer 46/137 Healthy/control 18/137
Other ST 137 1,156,046
112/137
 Curated
HNSCC_41616773 PCF discovery cohort
HNSCCDiscovery_41616773__PCF_CODEX
Head and neck 189/390 Lymph node metastasis 138/390 Lymphoid tissue 63/390
Primary cancer 189/390 Metastatic cancer 138/390 Healthy/control 63/390
CODEX 390 1,556,569
390/390
 Curated
HNSCC_41616773 PCF validation cohort
HNSCCValidation_41616773__PCF_CODEX
Head and neck 11/34 Lymph node metastasis 10/34 Lymphoid tissue 13/34
Primary cancer 15/34 Metastatic cancer 10/34 Healthy/control 9/34
CODEX 34 745,842
13/34
 Curated
LUAD_36725934 · IMC / Imaging Mass Cytometry
LUAD_36725934__IMC
Lung 416
Primary cancer 416
IMC 416 1,635,722
415/416
 Curated
Melanoma_35363543 · IMC / Imaging Mass Cytometry
Melanoma_35363543__IMC
Bone marrow 1/72 Brain 4/72 Large intestine 5/72 Lymph node metastasis 20/72 Skin 42/72
Primary cancer 31/72 Metastatic cancer 29/72 Healthy/control 12/72
IMC 72 272,135
72/72
 Curated
Melanoma_40148341 · CosMx SMI / NanoString SMI
Melanoma_40148341__CosMx_SMI
Skin 25
Primary cancer 25
CosMx 25 56,761
25/25
 Curated
Melanoma_41916292 · CyCIF / Cyclic IF
Melanoma_41916292__CyCIF
Skin 31
Primary cancer 31
CyCIF 31 3,293,552
2/31
 Curated
NSCLC_38242124 · IMC / Imaging Mass Cytometry
NSCLC_38242124__IMC
Lung 2,070
Primary cancer 2,070
IMC 2,070 5,984,454
2069/2070
 Curated
NSCLC_40408481 · PCF / CODEX / PhenoCycler Fusion
NSCLC_40408481__PCF_CODEX
Lung 257
Primary cancer 257
CODEX 257 1,450,507
257/257
 Curated
Neuroblastoma_41918107 · PCF / CODEX / PhenoCycler Fusion
Neuroblastoma_41918107__PCF_CODEX
Adrenal gland 24
Primary cancer 24
CODEX 24 832,243
0/24
 Curated
OSCC_41707652 · IMC / Imaging Mass Cytometry
OSCC_41707652__IMC
Head and neck 92
Primary cancer 92
IMC 92 708,261
92/92
 Curated
PDAC_39227743 · CosMx SMI / NanoString SMI
PDAC_39227743__CosMx_SMI
Pancreas 16
Primary cancer 16
CosMx 16 717,493
0/16
 Curated
PDAC_40269162 · CosMx SMI / NanoString SMI
PDAC_40269162__CosMx_SMI
Pancreas 90
Primary cancer 90
CosMx 90 82,348
84/90
 Curated
SPATCH_41107232 · CosMx SMI / NanoString SMI
SPATCH_41107232__CosMx_SMI
Large intestine 1/3 Liver 1/3 Ovary 1/3
Primary cancer 3
CosMx 3 818,673
0/3
 Curated