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Xenium Spatial transcriptomics Curated

Xenium Human Breast Gene Expression Panel 10x Genomics showcase

Dataset key: XeniumBreast_10xGenomics__Xenium

Breast 6

Disease detail: Primary cancer: Breast cancer (invasive ductal carcinoma)

Primary cancer 6

Samples

6

Cells

3,652,654

Curation

Curated

DEG

NA

Spatial

0/6

Open dataset

Xenium Spatial transcriptomics Curated

Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase

Dataset key: XeniumBreastJanesick_10xGenomics__Xenium

Breast 12

Disease detail: Primary cancer: Breast cancer (DCIS, ER+/PR+/HER2-2+), Healthy/control: Healthy human

Primary cancer 11/12 Healthy/control 1/12

Samples

12

Cells

3,442,976

Curation

Curated

DEG

NA

Spatial

0/12

Open dataset

Atera Spatial transcriptomics Curated

10x Genomics Atera showcase

Dataset key: Atera_10xGenomics__Atera

Breast 1/2 Uterus/Cervix 1/2

Disease detail: Primary cancer: Breast cancer (ductal carcinoma in situ, HER2-1+)

Primary cancer 2

Samples

2

Cells

887,633

Curation

Curated

DEG

NA

Spatial

0/2

Open dataset

Visium HD Spatial transcriptomics Curated

10x Genomics Visium HD p2 TMA showcase

Dataset key: VisiumHD_p2_TMA__Visium_HD

Breast 36

Disease detail: Primary cancer: Breast cancer

Primary cancer 36

Samples

36

Cells

117,494

Curation

Curated

DEG

NA

Spatial

33/36

Open dataset

Visium HD Spatial transcriptomics Curated

10x Genomics Visium HD p2 TissueArray showcase

Dataset key: VisiumHD_p2_TissueArray__Visium_HD

Breast 1/3 Large intestine 1/3 Lung 1/3

Disease detail: Primary cancer: Breast cancer (invasive ductal carcinoma)

Primary cancer 3

Samples

3

Cells

506,235

Curation

Curated

DEG

NA

Spatial

0/3

Open dataset

Visium HD Spatial transcriptomics Curated

10x Genomics Visium HD showcase

Dataset key: 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

Disease detail: Primary cancer: Colorectal cancer (adenocarcinoma), Healthy/control: Healthy human

Primary cancer 20/24 Healthy/control 4/24

Samples

24

Cells

5,379,712

Curation

Curated

DEG

NA

Spatial

0/24

Open dataset

Xenium Spatial transcriptomics Curated

10x Genomics Xenium Prime 5K showcase

Dataset key: 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

Disease detail: Primary cancer: Ovarian cancer (papillary serous carcinoma), Non-cancer disease: Reactive lymph node

Primary cancer 8/9 Non-cancer disease 1/9

Samples

9

Cells

4,598,042

Curation

Curated

DEG

NA

Spatial

0/9

Open dataset

IMC / Imaging Mass Cytometry Spatial proteomics Curated

BRCA_31959985 · IMC / Imaging Mass Cytometry

Dataset key: BRCA_31959985__IMC

Breast 376/381 Liver 5/381

Disease detail: Primary cancer: Breast cancer, Healthy/control: Normal/healthy breast tissue control

Primary cancer 289/381 Healthy/control 92/381

Samples

381

Cells

855,668

Curation

Curated

DEG

NA

Spatial

373/381

Open dataset

MIBI-TOF / Multiplexed Ion Beam Imaging Spatial proteomics Curated

BRCA_35063072 · MIBI-TOF / Multiplexed Ion Beam Imaging

Dataset key: BRCA_35063072__MIBI_TOF

Breast 79

Disease detail: Primary cancer: Breast cancer (ductal carcinoma in situ), Healthy/control: Normal/healthy breast tissue control

Primary cancer 70/79 Healthy/control 9/79

Samples

79

Cells

69,672

Curation

Curated

DEG

Available

Spatial

79/79

Open dataset

IMC / Imaging Mass Cytometry Spatial proteomics Curated

BRCA_35122013 · IMC / Imaging Mass Cytometry

Dataset key: BRCA_35122013__IMC

Breast 548

Disease detail: Primary cancer: Breast cancer

Primary cancer 548

Samples

548

Cells

479,844

Curation

Curated

DEG

Caveat

Spatial

547/548

Open dataset

CosMx SMI / NanoString SMI Spatial transcriptomics Curated

Bruker CosMx WTx FFPE showcase

Dataset key: CosMxWTx_Bruker__CosMx_SMI

Brain 1/9 Breast 2/9 Kidney 1/9 Large intestine 1/9 Pancreas 3/9 Skin 1/9

Disease detail: Primary cancer: Breast cancer, Healthy/control: Normal/healthy pancreas control

Primary cancer 5/9 Healthy/control 4/9

Samples

9

Cells

2,878,028

Curation

Curated

DEG

NA

Spatial

0/9

Open dataset

MERFISH / MERSCOPE Spatial transcriptomics Curated

MERFISH 500-plex Vizgen showcase

Dataset key: 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

Disease detail: Primary cancer: Ovarian cancer

Primary cancer 18

Samples

18

Cells

10,196,835

Curation

Curated

DEG

NA

Spatial

0/18

Open 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

Brain
Spinal cord
Head and neck
Lymphoid tissue
Musculoskeletal
Skin
Breast
Lung
Liver
Adrenal gland
Kidney
Bladder
Pancreas
Small intestine
Large intestine
Ovary
Prostate
Uterus/Cervix
Bone marrow
Heart

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
Healthy/control lung
Healthy/normal skin
Healthy adult human intestine
Healthy colon control
Healthy human
Healthy intestine
Hepatocellular carcinoma
High-grade serous carcinoma
IgA nephropathy
Inflammatory bowel disease
Intrahepatic cholangiocarcinoma
Kidney cancer
Kidney cancer (papillary renal cell carcinoma)
Kidney cancer (renal cell carcinoma)
Kidney disease (AA amyloid)
Kidney disease (C3GN)
Kidney disease (CKD)
Kidney disease (DKD)
Kidney disease (DKD+FSGS)
Kidney disease (DM)
Kidney disease (DM/HTN)
Kidney disease (FSGS)
Kidney disease (HTN)
Kidney disease (IgA)
Kidney disease (MN)
Kidney disease (TMA)
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
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