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
Melanoma_41916292 · CyCIF / Cyclic IF
Melanoma_41916292__CyCIF
Skin 31
Primary cancer 31
CyCIF 31 3,293,552
29/31
 Curated
NSCLC_38242124 · IMC / Imaging Mass Cytometry
NSCLC_38242124__IMC
Lung 2,070
Primary cancer 2,070
IMC 2,070 5,984,454
0/2070
 Curated
NSCLC_40408481 · PCF / CODEX / PhenoCycler Fusion
NSCLC_40408481__PCF_CODEX
Lung 257
Primary cancer 257
CODEX 257 1,450,507
257/257
 Curated
Neocortex_39779846 · MERFISH / MERSCOPE
Neocortex_39779846__MERFISH
Brain 6
Healthy/control 6
MERFISH 6 404,030
0/6
 Curated
Neuroblastoma_41918107 · PCF / CODEX / PhenoCycler Fusion
Neuroblastoma_41918107__PCF_CODEX
Adrenal gland 24
Primary cancer 24
CODEX 24 832,243
24/24
 Curated
NormalSkin_41872488 · MERFISH / MERSCOPE
NormalSkin_41872488__MERFISH
Skin 114
Healthy/control 114
MERFISH 114 1,201,886
0/114
 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
PulmonaryFibrosis_39901013 · Xenium
PulmonaryFibrosis_39901013__Xenium
Lung 45
Non-cancer disease 35/45 Healthy/control 10/45
Xenium 45 790,934
0/45
 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
2/3
 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
5/9
 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
1/3
 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
1/3
 Curated
SpinalCord_38513664 · ISS / In Situ Sequencing
SpinalCord_38513664__ISS
Spinal cord 52
Non-cancer disease 52
ISS 52 592,421
52/52
 Curated
SpinalCord_38513664 · Xenium
SpinalCord_38513664__Xenium
Spinal cord 6
Non-cancer disease 4/6 Healthy/control 2/6
Xenium 6 660,801
6/6
 Curated
TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion
TNBC_38194915__PCF_CODEX
Breast 27
Primary cancer 27
CODEX 27 2,597,738
27/27
 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
3/3
 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
8/12
 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
3/5
 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
17/20
 Curated
cHL_41923627 · CosMx SMI / NanoString SMI
cHL_41923627__CosMx_SMI
Lymphoid tissue 43
Primary cancer 43
CosMx 43 266,199
43/43
 Curated
cHL_41923627 · MIBI-TOF / Multiplexed Ion Beam Imaging
cHL_41923627__MIBI_TOF
Lymphoid tissue 9
Primary cancer 9
MIBI 9 1,409,210
1/9
 Curated
cHL_41923627 · PCF / CODEX / PhenoCycler Fusion
cHL_41923627__PCF_CODEX
Lymphoid tissue 27
Primary cancer 27
CODEX 27 934,478
27/27
 Curated