Datasets – Open Problems in Single Cell Analysis

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

tenx_visium/post_xenium/human_colon_cancer
10x Genomics (2023)
82.81 MiB
23-09-2024
5561 × 14016

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

tenx_visium/post_xenium/mouse_brain
10x Genomics (2023)
126.5 MiB
23-09-2024
5302 × 13883

10X Visium - Adult Human Cerebellum

Human Cerebellum Whole Transcriptome Analysis

tenx_visium/visium/human_cerebellum
10x Genomics (2020)
69.33 MiB
23-09-2024
4962 × 14782

10X Visium - Human Brain Cancer

Gene expression library of Human Glioblastoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_brain_cancer
10x Genomics (2023)
220 MiB
23-09-2024
10868 × 18016

10X Visium - Human Breast Cancer 1

Whole transcriptome analysis, Adult Human Breast Cancer (Visium)

tenx_visium/visium/human_breast_cancer_1
10x Genomics (2020)
75.53 MiB
23-09-2024
4263 × 14906

10X Visium - Human Breast Cancer 2

Gene expression library of Human Breast Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_breast_cancer_2
10x Genomics (2021)
55.79 MiB
23-09-2024
2518 × 13311

10X Visium - Human Cervical Cancer

Gene expression library of Human Cervical Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_cervical_cancer
10x Genomics (2022)
77.12 MiB
23-09-2024
2781 × 13866

10X Visium - Human Colorectal Cancer

ene expression library of Human Colorectal Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_colorectal_cancer
10x Genomics (2023)
341.68 MiB
23-09-2024
9079 × 18026

10X Visium - Human Heart

tenx_visium/visium/human_heart
10x Genomics (2019)
42.11 MiB
23-09-2024
4224 × 11564

10X Visium - Human Heart MI 1

Gene expression library of human heart using 10x Visium

zenodo_spatial/visium/human_heart_myocardial_infarction_1
Kuppe et al. (2022)
45.2 MiB
23-09-2024
4269 × 13236

10X Visium - Human Heart MI 2

Gene expression library of human heart using 10x Visium.

zenodo_spatial/visium/human_heart_myocardial_infarction_2
Kuppe et al. (2022)
24.46 MiB
23-09-2024
4518 × 10687

10X Visium - Human Intestine Cancer

Gene expression library of Human Intestinal Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_intestinal_cancer
10x Genomics (2022)
78.32 MiB
23-09-2024
2660 × 14292

10X Visium - Human Kidney

Gene expression library of Human Kidney (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_kidney
10x Genomics (2023)
144.88 MiB
23-09-2024
5935 × 18009

10X Visium - Human Lung Cancer

Gene expression library of Human Lung Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_lung_cancer
10x Genomics (2023)
270.93 MiB
23-09-2024
6195 × 18033

10X Visium - Human Lymph Node

Whole transcriptome analysis, Human Lymph Node

tenx_visium/visium/human_lymph_node
10x Genomics (2019)
93.98 MiB
23-09-2024
4037 × 15493

10X Visium - Human Normal Prostate

Gene expression library of Human Normal Prostate (Visium FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_normal_prostate
10x Genomics (2021)
37.44 MiB
23-09-2024
2543 × 13046

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

tenx_visium/visium/human_prostate_cancer
10x Genomics (2022)
72.38 MiB
23-09-2024
3460 × 13565

10X Visium - Human Skin Melanoma

Gene expression library of Human Skin Melanoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium/visium/human_skin_melanoma
10x Genomics (2022)
97.92 MiB
23-09-2024
3455 × 17874

10X Visium - Mouse Brain Coronal

Gene expression library of Mouse Brain (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set

tenx_visium/visium/mouse_brain_coronal
10x Genomics (2022)
66.22 MiB
23-09-2024
2310 × 13985

10X Visium - Mouse Embryo

Gene expression library of Mouse Embryo (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set

tenx_visium/visium/mouse_embryo
10x Genomics (2023)
246.08 MiB
23-09-2024
6434 × 19288

10X Visium - Mouse Kidney 1

Mouse Kidney Whole Transcriptome Analysis

tenx_visium/visium/mouse_kidney_v1
10x Genomics (2020)
45.12 MiB
23-09-2024
1435 × 14322

10X Visium - Mouse Olfactory Bulb

10X Genomics obtained fresh frozen mouse olfactory bulb tissue from BioIVT

tenx_visium/visium/mouse_olfactory_bulb
10x Genomics (2022)
29.91 MiB
23-09-2024
1184 × 13291

1k PBMCs

1k peripheral blood mononuclear cells from a healthy donor

openproblems_v1

openproblems_v1/tenx_1k_pbmc
10x Genomics (2018)
45.29 MiB
02-02-2024
1087 × 15099

5k PBMCs

5k peripheral blood mononuclear cells from a healthy donor

openproblems_v1

openproblems_v1/tenx_5k_pbmc
10x Genomics (2019)
156.82 MiB
02-02-2024
5247 × 20822

CITE-Seq CBMC

CITE-seq profiles of 8k Cord Blood Mononuclear Cells

openproblems_v1_multimodal

openproblems_v1_multimodal/citeseq_cbmc
Stoeckius et al. (2017)
191.3 MiB
02-02-2024
8617 × 36280

CeNGEN

Complete Gene Expression Map of an Entire Nervous System

openproblems_v1

openproblems_v1/cengen
Hammarlund et al. (2018)
778.17 MiB
02-02-2024
100955 × 22469

DBiT-seq - Mouse Brain (E10)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

zenodo_spatial/dbitseq/mouse_e10_brain
Liu et al. (2020)
6.44 MiB
23-09-2024
1789 × 5725

DBiT-seq - Mouse Eye (E10)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

zenodo_spatial/dbitseq/mouse_e10_eye
Liu et al. (2020)
22.62 MiB
23-09-2024
2500 × 12130

DBiT-seq - Mouse Lower Body (E11)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

zenodo_spatial/dbitseq/mouse_e11_lower_body
Liu et al. (2020)
14.88 MiB
23-09-2024
1662 × 10846

DBiT-seq - Mouse Whole Body (E10)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

zenodo_spatial/dbitseq/mouse_e10_whole_body
Liu et al. (2020)
13.86 MiB
23-09-2024
936 × 12047

DBiT-seq - Mouse Whole Body 1 (E11)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

zenodo_spatial/dbitseq/mouse_e11_1
Liu et al. (2020)
8.29 MiB
23-09-2024
1840 × 7068

DBiT-seq - Mouse Whole Body 2 (E11)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

zenodo_spatial/dbitseq/mouse_e11_2
Liu et al. (2020)
9.09 MiB
23-09-2024
2109 × 7178

Diabetic Kidney Disease

Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression

cellxgene_census

cellxgene_census/dkd
Wilson et al. (2022)
1.28 GiB
02-02-2024
39176 × 27980

GTEX v9

Single-nucleus cross-tissue molecular reference maps to decipher disease gene function

cellxgene_census

cellxgene_census/gtex_v9
Eraslan et al. (2022)
2.99 GiB
02-02-2024
209126 × 28094

Human Lung Cell Atlas

An integrated cell atlas of the human lung in health and disease (core)

cellxgene_census

cellxgene_census/hlca
Sikkema et al. (2023)
17.35 GiB
02-02-2024
584944 × 28024

Human immune

Human immune cells dataset from the scIB benchmarks

openproblems_v1

openproblems_v1/immune_cells
Luecken et al. (2021)
1.18 GiB
02-02-2024
33506 × 12303

Human pancreas

Human pancreas cells dataset from the scIB benchmarks

openproblems_v1

openproblems_v1/pancreas
Luecken et al. (2021)
1.26 GiB
02-02-2024
16382 × 18771

HypoMap

A unified single cell gene expression atlas of the murine hypothalamus

cellxgene_census

cellxgene_census/hypomap
Steuernagel et al. (2022)
12.58 GiB
02-02-2024
384925 × 41642

Immune Cell Atlas

Cross-tissue immune cell analysis reveals tissue-specific features in humans

cellxgene_census

cellxgene_census/immune_cell_atlas
Domínguez Conde et al. (2022)
9.7 GiB
02-02-2024
329762 × 29335

MERFISH - Human Cortex 1

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH)

zenodo_spatial/merfish/human_cortex_1
Fang et al. (2022)
8.78 MiB
23-09-2024
9259 × 247

MERFISH - Human Cortex 2

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH)

zenodo_spatial/merfish/human_cortex_2
Fang et al. (2022)
10.53 MiB
23-09-2024
3044 × 3546

MERFISH - Human Cortex 3

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH)

cellxgene_census

zenodo_spatial/merfish/human_cortex_3
Fang et al. (2022)
12.03 MiB
23-09-2024
4045 × 3591

MERFISH - Human Cortex 4

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH)

zenodo_spatial/merfish/human_cortex_4
Fang et al. (2022)
11.07 MiB
23-09-2024
3970 × 3511

MERFISH - Mouse Cortex

Spatially resolved profiling of mouse cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH)

zenodo_spatial/merfish/mouse_cortex
Fang et al. (2022)
12.54 MiB
23-09-2024
13221 × 234

Mouse Brain Atlas

Adult mouse primary visual cortex

openproblems_v1

openproblems_v1/allen_brain_atlas
Tasic et al. (2016)
1.91 GiB
02-02-2024
14249 × 34617

Mouse HSPC

Haematopoeitic stem and progenitor cells from mouse bone marrow

openproblems_v1

openproblems_v1/mouse_hspc_nestorowa2016
Nestorowa et al. (2016)
377.81 MiB
02-02-2024
1920 × 43258

Mouse Pancreatic Islet Atlas

Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes

cellxgene_census

cellxgene_census/mouse_pancreas_atlas
Hrovatin et al. (2023)
13.07 GiB
02-02-2024
301796 × 24923

Mouse myeloid

Myeloid lineage differentiation from mouse blood

openproblems_v1

openproblems_v1/mouse_blood_olsson_labelled
Olsson et al. (2016)
117.4 MiB
02-02-2024
660 × 116918

OpenProblems NeurIPS2021 CITE-Seq

Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors.

openproblems_neurips2021

openproblems_neurips2021/bmmc_cite
Luecken et al. (2021)
2.2 GiB
14-02-2024
90261 × 13953

OpenProblems NeurIPS2021 Multiome

Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors.

openproblems_neurips2021

openproblems_neurips2021/bmmc_multiome
Luecken et al. (2021)
7.78 GiB
14-02-2024
69249 × 13431

STARmap - Mouse Brain 1

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

zenodo_spatial/starmap/mouse_brain_2d_zstep10_0
Wang et al. (2018)
1.53 MiB
23-09-2024
2764 × 28

STARmap - Mouse Brain 2

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

zenodo_spatial/starmap/mouse_brain_2d_zstep15_0
Wang et al. (2018)
2.5 MiB
23-09-2024
4666 × 28

Seqfish - Mouse Organogenesis

Single-cell spatial expression of mouse organogenesis

zenodo_spatial/seqfish/mouse_organogenesis_seqfish
Lohoff et al. (2021)
15.53 MiB
23-09-2024
19402 × 351

Slide-seqV2 - Mouse Cerebellum

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

zenodo_spatial/slideseqv2/mouse_cerebellum
Stickels et al. (2020)
48.97 MiB
23-09-2024
25258 × 5205

Slide-seqV2 - Mouse Cortex

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

zenodo_spatial/slideseqv2/mouse_cortex
Stickels et al. (2020)
22.42 MiB
23-09-2024
17797 × 127

Slide-seqV2 - Mouse Hippocampus Puck

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

zenodo_spatial/slideseqv2/mouse_hippocampus_puck
Stickels et al. (2020)
98.93 MiB
23-09-2024
29309 × 8442

Slide-seqV2 - Mouse Olfactory Bulb Puck

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

zenodo_spatial/slideseqv2/mouse_olfactory_bulb_puck
Stickels et al. (2020)
37.54 MiB
23-09-2024
21624 × 4165

Slide-seqV2 - Mouse Somatosensory Cortex Puck

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

zenodo_spatial/slideseqv2/mouse_somatosensory_cortex_puck
Stickels et al. (2020)
62.1 MiB
23-09-2024
21941 × 6420

Slide-tags - Human Cortex

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

zenodo_spatial_slidetags

zenodo_spatial_slidetags/slidetags/human_cortex
Russell et al. (2023)
74.95 MiB
23-09-2024
4065 × 18570

Slide-tags - Human Skin Melanoma

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

zenodo_spatial_slidetags

zenodo_spatial_slidetags/slidetags/human_skin_melanoma
Russell et al. (2023)
56.24 MiB
23-09-2024
4804 × 15624

Slide-tags - Human Tonsil

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

zenodo_spatial_slidetags

zenodo_spatial_slidetags/slidetags/human_tonsil
Russell et al. (2023)
109.57 MiB
23-09-2024
5778 × 17746

Slide-tags - Mouse Embryo

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

zenodo_spatial_slidetags

zenodo_spatial_slidetags/slidetags/mouse_embryo
Russell et al. (2023)
70.21 MiB
23-09-2024
4623 × 14649

Stereo-seq - Drosophila embryo E10

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution

zenodo_spatial/stereoseq/drosophila_embryo_e10
Wang et al. (2022)
1.96 MiB
23-09-2024
1110 × 752

Stereo-seq - Drosophila embryo E5_6

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution

zenodo_spatial/stereoseq/drosophila_embryo_e5_6
Wang et al. (2022)
2.28 MiB
23-09-2024
1263 × 822

Stereo-seq - Drosophila embryo E6_3

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution

zenodo_spatial/stereoseq/drosophila_embryo_e6_3
Wang et al. (2022)
2.23 MiB
23-09-2024
1248 × 873

Stereo-seq - Drosophila embryo E7

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution

zenodo_spatial/stereoseq/drosophila_embryo_e7
Wang et al. (2022)
1.78 MiB
23-09-2024
1039 × 755

Stereo-seq - Drosophila embryo E9_1

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution

zenodo_spatial/stereoseq/drosophila_embryo_e9_1
Wang et al. (2022)
1.87 MiB
23-09-2024
1078 × 811

Tabula Sapiens

A multiple-organ, single-cell transcriptomic atlas of humans

cellxgene_census

cellxgene_census/tabula_sapiens
Jones et al. (2022)
19.17 GiB
02-02-2024
483152 × 55904

Triple-Negative Breast Cancer

1535 cells from six fresh triple-negative breast cancer tumors.

openproblems_v1

openproblems_v1/tnbc_wu2021
Wu et al. (2021)
1.18 GiB
02-02-2024
42512 × 28200

Zebrafish embryonic cells

Single-cell mRNA sequencing of zebrafish embryonic cells.

openproblems_v1

openproblems_v1/zebrafish
Wagner et al. (2018)
777.92 MiB
02-02-2024
26022 × 25258

sci-CAR Cell Lines

sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)

openproblems_v1_multimodal

openproblems_v1_multimodal/scicar_cell_lines
Cao et al. (2018)
205.41 MiB
02-02-2024
4739 × 60550

sci-CAR Mouse Kidney

sci-CAR profiles of 11k mouse kidney cells

openproblems_v1_multimodal

openproblems_v1_multimodal/scicar_mouse_kidney
Cao et al. (2018)
423 MiB
02-02-2024
11296 × 29013