scAtria single-cell spatial atlas resource

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Dataset Sample
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80 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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Curated only × 80 matches 80 curated
Dataset Organs ?For mixed datasets, fractions show sample counts per organ. Disease state Technique Samples Cells Spatial module Curation
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
0/36
 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 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
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
21/24
 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
4/9
 Curated
B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion
B-NHL_38379051__PCF_CODEX
Lymphoid tissue 35
Primary cancer 35
CODEX 35 5,690,284
35/35
 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
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
0/32
 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
387/393
 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
Bruker CosMx 64-protein FFPE showcase
CosMx64_Bruker__CosMx_SMI_protein
Breast 1/2 Lymphoid tissue 1/2
Healthy/control 2
CosMx-P 2 1,398,757
0/2
 Curated
Bruker CosMx 6k FFPE showcase
CosMx6k_Bruker__CosMx_SMI
Brain 1/2 Lymphoid tissue 1/2
Healthy/control 2
CosMx 2 2,041,632
1/2
 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
4/9
 Curated
CML_41592325 · PCF / CODEX / PhenoCycler Fusion
CML_41592325__PCF_CODEX
Bone marrow 55
Primary cancer 55
CODEX 55 2,033,725
55/55
 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
CastlemanDisease_40593805 · Xenium
CastlemanDisease_40593805__Xenium
Lymphoid tissue 18
Non-cancer disease 18
Xenium 18 1,299,746
18/18
 Curated
CervicalCancer_CmTSA_41807362
CervicalCancer_CmTSA_41807362__CmTSA
Uterus/Cervix 2
Primary cancer 2
CmTSA 2 1,564,537
0/2
 Curated
CutaneousLeishmaniasis_40371647 · CosMx SMI / NanoString SMI
CutaneousLeishmaniasis_40371647__CosMx_SMI
Skin 4
Non-cancer disease 4
CosMx 4 130,801
4/4
 Curated
DKD_42056516 · CosMx SMI / NanoString SMI
DKD_42056516__CosMx_SMI
Kidney 48
Non-cancer disease 36/48 Healthy/control 12/48
CosMx 48 3,386,822
48/48
 Curated
DKD_42056516 · Xenium
DKD_42056516__Xenium
Kidney 16
Non-cancer disease 13/16 Healthy/control 3/16
Xenium 16 951,040
16/16
 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
30/30
 Curated
HCC_39304772 · PCF / CODEX / PhenoCycler Fusion
HCC_39304772__PCF_CODEX
Liver 124
Primary cancer 124
CODEX 124 1,065,284
124/124
 Curated
HCC_39327501 · PCF / CODEX / PhenoCycler Fusion
HCC_39327501__PCF_CODEX
Liver 288
Primary cancer 288
CODEX 288 3,231,437
288/288
 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
31/31
 Curated
HGSC_39179931 · CosMx SMI / NanoString SMI
HGSC_39179931__CosMx_SMI
Ovary 166
Primary cancer 166
CosMx 166 1,724,825
165/166
 Curated
HGSC_39179931 · MERFISH / MERSCOPE
HGSC_39179931__MERFISH
Ovary 4
Primary cancer 4
MERFISH 4 425,578
4/4
 Curated
HGSC_39179931 · Xenium
HGSC_39179931__Xenium
Ovary 32
Primary cancer 32
Xenium 32 447,874
32/32
 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
137/137
 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 healthy lymph node cohort
HNSCCHealthyLN_41616773__PCF_CODEX
Lymphoid tissue 51
Healthy/control 51
CODEX 51 1,238,209
50/51
 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
34/34
 Curated
IBD_42049732 · CosMx SMI / NanoString SMI
IBD_42049732__CosMx_SMI
Large intestine 34
Non-cancer disease 34
CosMx 34 43,034
34/34
 Curated
Intestine_37468586 · PCF / CODEX / PhenoCycler Fusion
Intestine_37468586__PCF_CODEX
Large intestine 27/66 Small intestine 39/66
Healthy/control 66
CODEX 66 2,603,217
0/66
 Curated
Intestine_39843748 · MERFISH / MERSCOPE
Intestine_39843748__MERFISH
Large intestine 2
Healthy/control 2
MERFISH 2 470,081
2/2
 Curated
Intestine_39843748 · Xenium
Intestine_39843748__Xenium
Large intestine 16
Healthy/control 16
Xenium 16 2,814,759
14/16
 Curated
LUAD_36725934 · IMC / Imaging Mass Cytometry
LUAD_36725934__IMC
Lung 416
Primary cancer 416
IMC 416 1,635,722
415/416
 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
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
5/18
 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
5/6
 Curated
MERFISH 960-plex Vizgen showcase
MERFISH_960_Vizgen__MERFISH
Brain 3
Non-cancer disease 2/3 Healthy/control 1/3
MERFISH 3 394,181
3/3
 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