scAtria single-cell spatial atlas resource

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Dataset Sample
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21 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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Organ: Large intestine × Curated only × 21 matches 21 curated
Dataset Organs ?For mixed datasets, fractions show sample counts per organ. Disease state Technique Samples Cells Spatial module Curation
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
0/24
 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
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
71/170
 Curated
CRC_41986711 · CosMx SMI / NanoString SMI
CRC_41986711__CosMx_SMI
Large intestine 352
Primary cancer 352
CosMx 352 629,446
350/352
 Curated
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
0/2
 Curated
Intestine_39843748 · Xenium
Intestine_39843748__Xenium
Large intestine 16
Healthy/control 16
Xenium 16 2,814,759
0/16
 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
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
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
SPATCH_41107232 · PCF / CODEX / PhenoCycler Fusion
SPATCH_41107232__PCF_CODEX
Large intestine 3/9 Liver 3/9 Ovary 3/9
Primary cancer 9
CODEX 9 1,970,702
0/9
 Curated
SPATCH_41107232 · Stereo-seq / Stereo-seq Spatial Transcriptomics
SPATCH_41107232__Stereo_seq
Large intestine 1/3 Liver 1/3 Ovary 1/3
Primary cancer 3
Stereo 3 1,071,400
0/3
 Curated
SPATCH_41107232 · Xenium
SPATCH_41107232__Xenium
Large intestine 1/3 Liver 1/3 Ovary 1/3
Primary cancer 3
Xenium 3 1,087,807
0/3
 Curated
UlcerativeColitis_38374043 CosMx 1000-plex Run 2 Longitudinal
UlcerativeColitisRun2_38374043__CosMx_SMI
Large intestine 73
Non-cancer disease 50/73 Healthy/control 23/73
CosMx 73 126,368
73/73
 Curated
UlcerativeColitis_38374043 CosMx 960-plex Run 1
UlcerativeColitisRun1_38374043__CosMx_SMI
Large intestine 17
Non-cancer disease 9/17 Healthy/control 8/17
CosMx 17 66,379
16/17
 Curated
Xenium Human Immuno-Oncology Profiling Panel showcase
XeniumImmune_10xGenomics__Xenium
Brain 1/5 Large intestine 1/5 Lung 1/5 Ovary 1/5 Pancreas 1/5
Primary cancer 5
Xenium 5 1,848,679
0/5
 Curated