Datasets
Public, version-controlled, gold-standard datasets used to evaluate methods across the benchmarks.
10X Post Xenium - Human Colon
Gene expression library of Post Xenium Human Colon Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set - Replicate 1
10X Post Xenium - Mouse Brain
Gene expression library of Post Xenium Mouse Brain (CytAssist Fresh Frozen) using the Mouse Whole Transcriptome Probe Set - Replicate 1
10X Visium - Adult Human Cerebellum
Human Cerebellum Whole Transcriptome Analysis
10X Visium - Human Brain Cancer
Gene expression library of Human Glioblastoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Breast Cancer 1
Whole transcriptome analysis, Adult Human Breast Cancer (Visium)
10X Visium - Human Breast Cancer 2
Gene expression library of Human Breast Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Cervical Cancer
Gene expression library of Human Cervical Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Colorectal Cancer
Gene expression library of Human Colorectal Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Heart
V1_Human_Heart
10X Visium - Human Heart MI 1
Gene expression library of human heart using 10x Visium.
10X Visium - Human Heart MI 2
Gene expression library of human heart using 10x Visium.
10X Visium - Human Intestine Cancer
Gene expression library of Human Intestinal Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Kidney
Gene expression library of Human Kidney (CytAssist FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Lung Cancer
Gene expression library of Human Lung Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Lymph Node
Whole transcriptome analysis, Human Lymph Node
10X Visium - Human Normal Prostate
Gene expression library of Human Normal Prostate (Visium FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Human Prostate Cancer
Gene expression library of Human Prostate Cancer (Visium FFPE) with an IF image using the Human Whole Transcriptome Probe Set
10X Visium - Human Skin Melanoma
Gene expression library of Human Skin Melanoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set
10X Visium - Mouse Brain Coronal
Gene expression library of Mouse Brain (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set
10X Visium - Mouse Embryo
Gene expression library of Mouse Embryo (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set
10X Visium - Mouse Kidney 1
Mouse Kidney Whole Transcriptome Analysis
10X Visium - Mouse Olfactory Bulb
10X Genomics obtained fresh frozen mouse olfactory bulb tissue from BioIVT.
1k Peripheral blood mononuclear cells
1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics.
5k Peripheral blood mononuclear cells
5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. 5247 cells x 20822 features with no cell type labels
DBiT-seq - Mouse Brain (E10)
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.
DBiT-seq - Mouse Eye (E10)
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.
DBiT-seq - Mouse Lower Body (E11)
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.
DBiT-seq - Mouse Whole Body (E10)
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.
DBiT-seq - Mouse Whole Body 1 (E11)
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.
DBiT-seq - Mouse Whole Body 2 (E11)
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.
Diabetic Kidney Disease
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression
GTEX v9
Single-nucleus cross-tissue molecular reference maps to decipher disease gene function
HypoMap
A unified single cell gene expression atlas of the murine hypothalamus
Immune Cell Atlas
Cross-tissue immune cell analysis reveals tissue-specific features in humans
MERFISH - Human Cortex 1
Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).
MERFISH - Human Cortex 2
Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).
MERFISH - Human Cortex 3
Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).
MERFISH - Human Cortex 4
Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).
MERFISH - Mouse Cortex
Spatially resolved profiling of mouse cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).
Mouse brain atlas
A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). 14249 cells x 34617 features with 23 cell type labels.
Mouse hematopoietic stem cell differentiation
1.6k hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. 1920 cells x 43258 features with 3 cell type labels
Mouse myeloid lineage differentiation
Myeloid lineage differentiation from mouse blood. Sequenced by SMARTseq in 2016 by Olsson et al. 660 cells x 112815 features with 4 cell type labels
Mouse Pancreatic Islet Atlas
Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes
Pancreas (alpha=0.5)
Human pancreas cells aggregated from single-cell (Dirichlet alpha=0.5)
Pancreas (alpha=1)
Human pancreas cells aggregated from single-cell (Dirichlet alpha=1)
Pancreas (alpha=5)
Human pancreas cells aggregated from single-cell (Dirichlet alpha=5)
Pancreas (inDrop)
Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Here we just use the inDrop1 batch, which includes1937 cells × 15502 genes.
Seqfish - Mouse Organogenesis
Single-cell spatial expression of mouse organogenesis.
Slide-seqV2 - Mouse Cerebellum
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Slide-seqV2 - Mouse Cortex
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Slide-seqV2 - Mouse Hippocampus Puck
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Slide-seqV2 - Mouse Olfactory Bulb Puck
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Slide-seqV2 - Mouse Somatosensory Cortex Puck
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Slide-tags - Human Cortex
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.
Slide-tags - Human Skin Melanoma
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.
Slide-tags - Human Tonsil
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.
Slide-tags - Mouse Embryo
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.
STARmap - Mouse Brain 1
Three-dimensional intact-tissue sequencing of single-cell transcriptional states.
STARmap - Mouse Brain 2
Three-dimensional intact-tissue sequencing of single-cell transcriptional states.
Stereo-seq - Drosophila embryo E10
Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.
Stereo-seq - Drosophila embryo E5_6
Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.
Stereo-seq - Drosophila embryo E6_3
Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.
Stereo-seq - Drosophila embryo E7
Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.
Stereo-seq - Drosophila embryo E9_1
Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.
Tabula Sapiens
A multiple-organ, single-cell transcriptomic atlas of humans
Zebrafish
90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084±1156 cells per cell type).