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single-cell spatial atlas resource
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Browse is the search page: type a query, then refine by organ, technique, modality, curation, and dataset/sample view.
Dataset
Sample
Card
Table
70 Samples
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Examples
Study ID
HNSCC_41616773
Modality
Spatial transcriptomics
Technique
Xenium
Organ
breast
Disease state
primary cancer
Disease detail
breast cancer
Filter scope
70 matches · sample view
Applied
Dataset
ASD_42288509 · MERFISH / MERSCOPE
10x Genomics Atera showcase
B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion
BoneMarrow_38714197 · PCF / CODEX / PhenoCycler Fusion
BrainTumor_36725935 · IMC / Imaging Mass Cytometry
BRCA_31959985 · IMC / Imaging Mass Cytometry
BRCA_35063072 · MIBI-TOF / Multiplexed Ion Beam Imaging
BRCA_35122013 · IMC / Imaging Mass Cytometry
CastlemanDisease_40593805 · Xenium
CervicalCancer_CmTSA_41807362
cHL_41923627 · CosMx SMI / NanoString SMI
cHL_41923627 · MIBI-TOF / Multiplexed Ion Beam Imaging
cHL_41923627 · PCF / CODEX / PhenoCycler Fusion
CML_41592325 · PCF / CODEX / PhenoCycler Fusion
Bruker CosMx 1k FFPE showcase
Bruker CosMx 64-protein FFPE showcase
Bruker CosMx 6k FFPE showcase
Bruker CosMx WTx FFPE showcase
CRC_32763154 · PCF / CODEX / PhenoCycler Fusion
CRC_40189697 · IMC / Imaging Mass Cytometry
CRC_41986711 · CosMx SMI / NanoString SMI
CRC_42167227 · CosMx SMI / NanoString SMI
CutaneousLeishmaniasis_40371647 · CosMx SMI / NanoString SMI
DevelopingLung_39477961 · PCF / CODEX / PhenoCycler Fusion
DKD_42056516 · CosMx SMI / NanoString SMI
DKD_42056516 · Xenium
DLBCL_41120574 · CosMx SMI / NanoString SMI
DLBCL_41874448 · CosMx SMI / NanoString SMI
DLBCL_41874448 · PCF / CODEX / PhenoCycler Fusion
GBM_40972572 · CosMx SMI Protein
HCC_39304772 · PCF / CODEX / PhenoCycler Fusion
HCC_39327501 · PCF / CODEX / PhenoCycler Fusion
HCC_39455893 · IMC / Imaging Mass Cytometry
HCC_39965889 · PCF / CODEX / PhenoCycler Fusion
LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI
HGSC_39179931 · CosMx SMI / NanoString SMI
HGSC_39179931 · MERFISH / MERSCOPE
HGSC_39179931 · Xenium
HGSOC_38570491 · CosMx SMI / NanoString SMI
HNSCC_41616773 · Other ST
HNSCC_41616773 PCF discovery cohort
HNSCC_41616773 PCF healthy lymph node cohort
HNSCC_41616773 PCF validation cohort
IBD_42049732 · CosMx SMI / NanoString SMI
LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI
IgAN_38898271 · Xenium
Intestine_37468586 · PCF / CODEX / PhenoCycler Fusion
Intestine_39843748 · MERFISH / MERSCOPE
Intestine_39843748 · Xenium
Liver_41986723 · MERFISH / MERSCOPE
LUAD_36725934 · IMC / Imaging Mass Cytometry
Melanoma_35363543 · IMC / Imaging Mass Cytometry
Melanoma_40148341 · CosMx SMI / NanoString SMI
Melanoma_40457060 · CosMx SMI / NanoString SMI
Melanoma_41916292 · CyCIF / Cyclic IF
MERFISH 500-plex Vizgen showcase
MERFISH 815-plex Vizgen showcase
MERFISH 960-plex Vizgen showcase
MIBC_42126225 · Xenium
Neocortex_39779846 · MERFISH / MERSCOPE
Neuroblastoma_41918107 · PCF / CODEX / PhenoCycler Fusion
NormalSkin_41872488 · MERFISH / MERSCOPE
NSCLC_38242124 · IMC / Imaging Mass Cytometry
NSCLC_40220761 · CosMx SMI / NanoString SMI
NSCLC_40408481 · PCF / CODEX / PhenoCycler Fusion
Oral_41663813 · Xenium
OSCC_41707652 · IMC / Imaging Mass Cytometry
PDAC_39227743 · CosMx SMI / NanoString SMI
PDAC_40269162 · CosMx SMI / NanoString SMI
PDAC_41916312 · Xenium
PulmonaryFibrosis_39901013 · Xenium
RheumatoidArthritis_39609125 · CosMx SMI / NanoString SMI
SCN_41720090 · MERFISH / MERSCOPE
SCN_41720090 · Visium HD
SPATCH_41107232 · CosMx SMI / NanoString SMI
SPATCH_41107232 · PCF / CODEX / PhenoCycler Fusion
SPATCH_41107232 · Stereo-seq / Stereo-seq Spatial Transcriptomics
SPATCH_41107232 · Xenium
SpinalCord_38513664 · ISS / In Situ Sequencing
SpinalCord_38513664 · Xenium
TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion
UlcerativeColitis_38374043 CosMx 960-plex Run 1
UlcerativeColitis_38374043 CosMx 1000-plex Run 2 Longitudinal
10x Genomics Visium HD showcase
10x Genomics Visium HD p2 TissueArray showcase
10x Genomics Visium HD p2 TMA showcase
10x Genomics Visium HD p2 WholeSlide showcase
10x Genomics Xenium Prime 5K showcase
Xenium Human Brain Gene Expression Panel showcase
Xenium Human Breast Gene Expression Panel 10x Genomics showcase
Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase
Xenium Human Immuno-Oncology Profiling Panel showcase
Xenium Human Lung Gene Expression Panel showcase
Xenium Human Multi-Tissue and Cancer Panel showcase
Organ
Filtered
x
Brain
Spinal cord
Head and neck
Lymphoid tissue
Musculoskeletal
Skin
Breast
Lung
Liver
Adrenal gland
Kidney (70)
Bladder
Pancreas
Small intestine
Large intestine
Ovary
Prostate
Uterus/Cervix
Bone marrow
Heart
Disease state
Healthy/control (17)
Primary cancer (3)
Metastatic cancer
Non-cancer disease (50)
Disease detail
Acute lymphoid leukemia
Acute myeloid leukemia
Adenosquamous lung carcinoma
Alzheimer's disease
Astrocytoma (Primary)
Astrocytoma (Progression from grade II/III)
Astrocytoma (Recurrent)
Autism spectrum disorder cortical organoid model
B-cell non-Hodgkin lymphoma
Brain metastasis
Brain metastasis from Bladder/urinary tract
Brain metastasis from Breast
Brain metastasis from extremity
Brain metastasis from Intestine
Brain metastasis from Lung
Brain metastasis from Ovary/Fallopian tube
Brain metastasis from Skin
Brain metastasis from Stomach/upper GI
Brain metastasis from trunk
Breast cancer
Breast cancer (CCH/DCIS, ER+/PR+/HER2-1+)
Breast cancer (DCIS, ER+/PR+/HER2-2+)
Breast cancer (DCIS, ER-/PR-/HER2-2+)
Breast cancer (DCIS, HER2-1+)
Breast cancer (DCIS, HER2-2+)
Breast cancer (DCIS, HER2-3+)
Breast cancer (ductal carcinoma in situ)
Breast cancer (ductal carcinoma in situ, HER2-1+)
Breast cancer (IDC, ER+/PR+/HER2-1+)
Breast cancer (IDC, ER+/PR+/HER2-2+)
Breast cancer (IDC, HER2-)
Breast cancer (invasive ductal carcinoma)
Breast cancer (invasive ductal carcinoma, ductal carcinoma in situ)
Breast cancer (invasive lobular carcinoma)
Castleman disease
Cervical Cancer
Cervical cancer
Cervical cancer (squamous cell carcinoma)
Chronic myeloid leukemia bone marrow
Classical Hodgkin lymphoma
Colorectal cancer
Colorectal cancer (adenocarcinoma)
Cutaneous leishmaniasis
Developing healthy lung
Diffuse large B-cell lymphoma
Experimental autoimmune encephalomyelitis (multiple sclerosis model)
Follicular lymphoid hyperplasia
Glioblastoma
Glioblastoma (Primary)
Glioblastoma (Progression from grade II/III)
Glioblastoma (Recurrent)
Glioblastoma (Residual)
Glioma, IDH status unknown (Primary)
Head and neck squamous cell carcinoma
Healthy/control kidney (15)
Healthy/control lung
Healthy/normal skin
Healthy adult human intestine
Healthy colon control
Healthy human (1)
Healthy intestine
Hepatocellular carcinoma
High-grade serous carcinoma
IgA nephropathy (1)
Inflammatory bowel disease
Intrahepatic cholangiocarcinoma
Kidney cancer (1)
Kidney cancer (papillary renal cell carcinoma) (1)
Kidney cancer (renal cell carcinoma) (1)
Kidney disease (AA amyloid) (2)
Kidney disease (C3GN) (1)
Kidney disease (CKD) (1)
Kidney disease (DKD) (29)
Kidney disease (DKD+FSGS) (1)
Kidney disease (DM) (6)
Kidney disease (DM/HTN) (4)
Kidney disease (FSGS) (1)
Kidney disease (HTN) (1)
Kidney disease (IgA) (1)
Kidney disease (MN) (1)
Kidney disease (TMA) (1)
Large-cell/other non-small cell lung cancer
Lung adenocarcinoma
Lung cancer
Lung cancer (invasive acinar adenocarcinoma)
Lung cancer (invasive adenocarcinoma)
Lung squamous cell carcinoma
Lymphoid tissue metastasis
Lymphoid tissue metastasis from acral
Lymphoid tissue metastasis from extremity
Lymphoid tissue metastasis from head/neck
Lymphoid tissue metastasis from Oral cavity
Lymphoid tissue metastasis from trunk
Melanocytic nevus / non-malignant skin control
Melanoma
Multiple sclerosis
Muscle-invasive bladder cancer
Neuroblastoma
Non-small cell lung cancer
Normal/healthy bone marrow control
Normal/healthy breast tissue control
Normal/healthy heart control
Normal/healthy hippocampus brain tissue
Normal/healthy kidney control (1)
Normal/healthy liver control
Normal/healthy pancreas control
Normal/healthy suprachiasmatic nucleus brain tissue
Normal/healthy tonsil control
Normal brain cortex
Normal developing human neocortex
Oral health
Oral squamous cell carcinoma
Organ-specific lymph-node control/no cancer
Organ-specific spinal-cord control/no cancer
Other non-small cell lung cancer
Ovarian cancer
Ovarian cancer (adenocarcinoma)
Ovarian cancer (clear cell adenocarcinoma)
Ovarian cancer (papillary serous carcinoma)
Pancreatic cancer
Pancreatic ductal adenocarcinoma
Periodontitis
Prostate cancer
Prostate cancer (adenocarcinoma)
Pulmonary fibrosis / interstitial lung disease (cHP)
Pulmonary fibrosis / interstitial lung disease (CPFE)
Pulmonary fibrosis / interstitial lung disease (CTD-ILD)
Pulmonary fibrosis / interstitial lung disease (ILD)
Pulmonary fibrosis / interstitial lung disease (IPAF)
Pulmonary fibrosis / interstitial lung disease (IPF)
Pulmonary fibrosis / interstitial lung disease (NSIP)
Pulmonary fibrosis / interstitial lung disease (Sarcoidosis)
Reactive Follicular Hyperplasia
Reactive follicular hyperplasia
Reactive lymph node
Rheumatoid arthritis (active)
Rheumatoid arthritis (remission)
Skin cancer
Skin metastasis
Skin metastasis from extremity
Skin metastasis from head/neck
Skin metastasis from trunk
Triple-negative breast cancer
Ulcerative colitis
Ulcerative colitis (post-vedolizumab, non-responder)
Ulcerative colitis (post-vedolizumab, responder)
Ulcerative colitis (pre-vedolizumab, non-responder)
Ulcerative colitis (pre-vedolizumab, responder)
Ulcerative colitis (vedolizumab-treated)
Uterine cancer
Technique
Atera
CmTSA
CosMx SMI / NanoString SMI (2)
CosMx SMI Protein
CyCIF / Cyclic IF
IMC / Imaging Mass Cytometry
ISS / In Situ Sequencing
MERFISH / MERSCOPE
MIBI-TOF / Multiplexed Ion Beam Imaging
Other ST
PCF / CODEX / PhenoCycler Fusion
Stereo-seq / Stereo-seq Spatial Transcriptomics
Visium HD (1)
Xenium (3)
Modality
Spatial proteomics
Spatial transcriptomics (6)
Sample
Visium_HD_10xGenomics__Visium_HD__Visium_HD_Human_Kidney_FFPE
CosMxWTx_Bruker__CosMx_SMI__CosMxKidneyCancerWTx_Bruker
DKD_42056516__CosMx_SMI__1061
DKD_42056516__CosMx_SMI__1062
DKD_42056516__CosMx_SMI__1063
DKD_42056516__CosMx_SMI__1064
DKD_42056516__CosMx_SMI__1068
DKD_42056516__CosMx_SMI__1070
DKD_42056516__CosMx_SMI__1071
DKD_42056516__CosMx_SMI__1072
DKD_42056516__CosMx_SMI__HK2695
DKD_42056516__CosMx_SMI__HK2753
DKD_42056516__CosMx_SMI__HK2841
DKD_42056516__CosMx_SMI__HK2844
DKD_42056516__CosMx_SMI__HK2844_2
DKD_42056516__CosMx_SMI__HK2873
DKD_42056516__CosMx_SMI__HK2874
DKD_42056516__CosMx_SMI__HK2924
DKD_42056516__CosMx_SMI__HK2989
DKD_42056516__CosMx_SMI__HK2990
DKD_42056516__CosMx_SMI__HK3035
DKD_42056516__CosMx_SMI__HK3035_2
DKD_42056516__CosMx_SMI__HK3039
DKD_42056516__CosMx_SMI__HK3063
DKD_42056516__CosMx_SMI__HK3066
DKD_42056516__CosMx_SMI__HK3068
DKD_42056516__CosMx_SMI__HK3069
DKD_42056516__CosMx_SMI__HK3070
DKD_42056516__CosMx_SMI__HK3106
DKD_42056516__CosMx_SMI__HK3421
DKD_42056516__CosMx_SMI__HK3469
DKD_42056516__CosMx_SMI__HK3474
DKD_42056516__CosMx_SMI__HK3531
DKD_42056516__CosMx_SMI__HK3531_2
DKD_42056516__CosMx_SMI__HK3535
DKD_42056516__CosMx_SMI__HK3542
DKD_42056516__CosMx_SMI__HK3565
DKD_42056516__CosMx_SMI__HK3588
DKD_42056516__CosMx_SMI__HK3591
DKD_42056516__CosMx_SMI__HK3594
DKD_42056516__CosMx_SMI__HK3606
DKD_42056516__CosMx_SMI__HK3612
DKD_42056516__CosMx_SMI__HK3614
DKD_42056516__CosMx_SMI__HK3616
DKD_42056516__CosMx_SMI__HK3623
DKD_42056516__CosMx_SMI__HK3624
DKD_42056516__CosMx_SMI__HK3626
DKD_42056516__CosMx_SMI__HK3631
DKD_42056516__CosMx_SMI__HK3647
DKD_42056516__CosMx_SMI__Pediatric1
DKD_42056516__Xenium__1001
DKD_42056516__Xenium__1003
DKD_42056516__Xenium__1004
DKD_42056516__Xenium__1005
DKD_42056516__Xenium__1006
DKD_42056516__Xenium__1007
DKD_42056516__Xenium__1008
DKD_42056516__Xenium__1009
DKD_42056516__Xenium__1010
DKD_42056516__Xenium__1011
DKD_42056516__Xenium__1012
DKD_42056516__Xenium__1013
DKD_42056516__Xenium__HK2695
DKD_42056516__Xenium__HK2753
DKD_42056516__Xenium__HK3106
DKD_42056516__Xenium__HK3626
XeniumMulti_10xGenomics__Xenium__Xenium_V1_hKidney_cancer_section
XeniumMulti_10xGenomics__Xenium__Xenium_V1_hKidney_nondiseased_section
XeniumMulti_10xGenomics__Xenium__Xenium_V1_Human_Kidney_FFPE_Protein_updated
IgAN_38898271__Xenium__GSM8216268
Curation
All
Curated
DEG
All
Public ready
Available
Caveat
Missing
Held
Spatial module
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Missing
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Sample
Organ
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Modality
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Spatial module
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Organ: Kidney
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70 matches
69 curated
Download sample CSV
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Sample
Organ
Disease state
Technique
Cells
Spatial module
Curation
DKD_42056516__Xenium__1001
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
29,126
D
I
T
Curated
DKD_42056516__Xenium__1003
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
30,772
D
I
T
Curated
DKD_42056516__Xenium__1004
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
24,449
D
I
T
Curated
DKD_42056516__Xenium__1005
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
17,937
D
T1
T2
T3
I
T1
T2
T3
T
T1
T2
T3
Curated
DKD_42056516__Xenium__1006
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
45,609
D
I
T
Curated
DKD_42056516__Xenium__1007
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
41,336
D
I
T
Curated
DKD_42056516__Xenium__1008
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
27,912
D
I
T
Curated
DKD_42056516__Xenium__1009
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
10,167
D
T1
T2
T3
I
T1
T2
T3
T
T1
T2
T3
Curated
DKD_42056516__Xenium__1010
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
40,475
D
I
T
Curated
DKD_42056516__Xenium__1011
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
27,876
D
I
T
Curated
DKD_42056516__Xenium__1012
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
39,105
D
I
T
Curated
DKD_42056516__Xenium__1013
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
28,261
D
I
T
Curated
DKD_42056516__Xenium__HK2695
DKD_42056516 · Xenium
Kidney
Non-cancer disease
Xenium
151,101
D
I
T
Curated
DKD_42056516__Xenium__HK2753
DKD_42056516 · Xenium
Kidney
Healthy/control
Xenium
161,350
D
I
T
Curated
DKD_42056516__Xenium__HK3106
DKD_42056516 · Xenium
Kidney
Healthy/control
Xenium
171,526
D
I
T
Curated
DKD_42056516__Xenium__HK3626
DKD_42056516 · Xenium
Kidney
Healthy/control
Xenium
104,038
D
I
T
Curated
XeniumMulti_10xGenomics__Xenium__Xenium_V1_hKidney_cancer_section
Xenium Human Multi-Tissue and Cancer Panel showcase
Kidney
Primary cancer
Xenium
56,510
D
I
T
Curated
XeniumMulti_10xGenomics__Xenium__Xenium_V1_hKidney_nondiseased_section
Xenium Human Multi-Tissue and Cancer Panel showcase
Kidney
Healthy/control
Xenium
97,560
D
I
T
Curated
XeniumMulti_10xGenomics__Xenium__Xenium_V1_Human_Kidney_FFPE_Protein_updated
Xenium Human Multi-Tissue and Cancer Panel showcase
Kidney
Primary cancer
Xenium
465,534
D
I
T
Curated
IgAN_38898271__Xenium__GSM8216268
IgAN_38898271 · Xenium
Kidney
Non-cancer disease
Xenium
30,802
D
I
T
Source
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