scAtria single-cell spatial atlas resource

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74 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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Search: Spatial transcriptomics × 74 matches 61 curated
Dataset Organs ?For mixed datasets, fractions show sample counts per organ. Disease state Technique Samples Cells Spatial module Curation
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
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 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
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
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 6k FFPE showcase
CosMx6k_Bruker__CosMx_SMI
Brain 1/2 Lymphoid tissue 1/2
Healthy/control 2
CosMx 2 2,041,632
0/2
 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
0/9
 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
5/18
 Curated
CutaneousLeishmaniasis_40371647 · CosMx SMI / NanoString SMI
CutaneousLeishmaniasis_40371647__CosMx_SMI
Skin 4
Non-cancer disease 4
CosMx 4 130,801
1/4
 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
8/48
 Curated
DKD_42056516 · Xenium
DKD_42056516__Xenium
Kidney 16
Non-cancer disease 13/16 Healthy/control 3/16
Xenium 16 951,040
2/16
 Curated
DLBCL_41874448 · CosMx SMI / NanoString SMI
DLBCL_41874448__CosMx_SMI
Lymphoid tissue 56
Primary cancer 56
CosMx 56 182,646
56/56
 Curated
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
27/32
 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
132/137
 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_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
LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI
HCC_41723121__CosMx_SMI
Liver 9
Primary cancer 9
CosMx 9 1,446,124
1/9
 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
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
MERFISH 960-plex Vizgen showcase
MERFISH_960_Vizgen__MERFISH
Brain 3
Non-cancer disease 2/3 Healthy/control 1/3
MERFISH 3 394,181
0/3
 Curated
Melanoma_40148341 · CosMx SMI / NanoString SMI
Melanoma_40148341__CosMx_SMI
Skin 25
Primary cancer 25
CosMx 25 56,761
25/25
 Curated
Neocortex_39779846 · MERFISH / MERSCOPE
Neocortex_39779846__MERFISH
Brain 6
Healthy/control 6
MERFISH 6 404,030
0/6
 Curated
NormalSkin_41872488 · MERFISH / MERSCOPE
NormalSkin_41872488__MERFISH
Skin 114
Healthy/control 114
MERFISH 114 1,201,886
103/114
 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
PulmonaryFibrosis_39901013 · Xenium
PulmonaryFibrosis_39901013__Xenium
Lung 45
Non-cancer disease 35/45 Healthy/control 10/45
Xenium 45 790,934
33/45
 Curated
SCN_41720090 · MERFISH / MERSCOPE
SCN_41720090__MERFISH
Brain 1
Healthy/control 1
MERFISH 1 6,953
1/1
 Curated
SCN_41720090 · Visium HD
SCN_41720090__Visium_HD
Brain 1
Healthy/control 1
Visium HD 1 16,123
1/1
 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 · 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
SpinalCord_38513664 · ISS / In Situ Sequencing
SpinalCord_38513664__ISS
Spinal cord 52
Non-cancer disease 52
ISS 52 592,421
44/52
 Curated
SpinalCord_38513664 · Xenium
SpinalCord_38513664__Xenium
Spinal cord 6
Non-cancer disease 4/6 Healthy/control 2/6
Xenium 6 660,801
0/6
 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
17/17
 Curated
Xenium Human Brain Gene Expression Panel showcase
XeniumBrain_10xGenomics__Xenium
Brain 3
Healthy/control 1/3 Non-cancer disease 1/3 Primary cancer 1/3
Xenium 3 110,248
0/3
 Curated
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
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
Xenium Human Lung Gene Expression Panel showcase
XeniumLung_10xGenomics__Xenium
Lung 3
Primary cancer 2/3 Healthy/control 1/3
Xenium 3 1,105,707
0/3
 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
cHL_41923627 · CosMx SMI / NanoString SMI
cHL_41923627__CosMx_SMI
Lymphoid tissue 43
Primary cancer 43
CosMx 43 266,199
43/43
 Curated