Single Cell Browser
Fast, interactive exploration of annotated single-cell RNA-seq data.
26 public datasets · 3,486,741 cells · Mus musculus, Homo sapiens, Cross-species (mouse, human, macaque, guinea pig)
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Public Datasets
26MAPPS 2022 - Satellite Glial Cells
Satellite glial cell subset from MAPPS peripheral ganglia study
View DatasetDeveloping Mouse Thalamus — Shh Perturbation
Single-cell atlas of the developing mouse thalamus and prethalamus (E12.5-E18.5), comparing control and Shh enhancer-deletion (dSBE1/5) embryos. Resolves reticular thalamus, zona incerta, prethalamic and caudal-thalamic neurons and progenitors, plus pretectum, habenula and hypothalamus. Govek et al., Cell Reports 2022.
View DatasetMouse Visual Thalamus — dLGN, vLGN & LP (SMART-Seq)
Plate-based SMART-Seq single-cell atlas of the adult mouse dorsal lateral geniculate nucleus (dLGN core and shell) together with the ventral LGN (vLGN) and lateral posterior (LP) nucleus. Resolves 15 neuronal and non-neuronal types including six GABAergic populations (several Sox14+), the LGd relay neurons, and vLGN/LP types. Mouse subset of the cross-species study of Bakken et al., eLife 2021.
View DatasetParaventricular Thalamus (PVT) & Surround — snRNA-seq
Single-nucleus RNA-seq atlas of the mouse paraventricular nucleus of the thalamus (PVT) and immediately surrounding regions (mediodorsal and intermediodorsal thalamus, principal nucleus of BST, habenula). 20,503 nuclei across 16 clusters spanning eight neuronal populations and the major glial and vascular classes. Gao et al., eLife 2023.
View DatasetLateral Habenula GAD2+ Neurons (snRNA-seq)
Single-nucleus RNA-seq of genetically enriched GAD2-lineage (Gad2-Cre;Sun1-GFP) nuclei from the mouse lateral habenula. Resolves the medial-LHb GAD2+/VGLUT2+ population (Slc32a1-negative, marker Ntng2), a canonical GABAergic interneuron population, neighbouring perihabenular/dorsal-thalamic and MHb-like neurons, and the Gad2-lineage glia. Green et al., Biol Psychiatry Global Open Science 2023. Note: the GEO deposit provides raw counts only; cell-type labels here were reproduced from the raw data following the published method and assigned by marker signature per the paper's identities (a derived reproduction, not a deposited annotation).
View DatasetHabenular Complex — MHb & LHb (scRNA-seq)
Single-cell RNA-seq of the mouse habenular complex (medial and lateral habenula). Resolves glutamatergic MHb neurons (Tac2+), a cholinergic MHb subset (Chat/Slc18a3+), LHb neurons (Gap43+), and the habenular glia. This dataset is the clearest evidence that the habenula lacks GABAergic neurons (no Slc32a1, low Gad2). Wallace et al., eLife 2020. Note: the deposit provides raw counts only; cell-type labels here were reproduced from the raw data following the published method and assigned by marker signature per the paper's identities (a derived reproduction, not a deposited annotation).
View DatasetTRN & Zona Incerta — P21 Dlx1/2 cKO (snRNA-seq)
Single-nucleus RNA-seq of the P21 mouse thalamic reticular nucleus (TRN) and zona incerta (ZI), comparing control and Foxd1-Cre; Dlx1/2 conditional-knockout mice. Resolves the two flagship GABAergic populations of the region — TRN neurons (Pvalb/Meis2) and ZI neurons (Sst/Penk) — alongside excitatory thalamic neurons (Slc17a6/Slc17a7), neighbouring hypothalamic neuron types caught in the microdissection, and glia. Loss of Dlx1/2 depletes the Pvalb/Meis2 and Sst/Penk GABAergic neurons and disrupts inhibition of excitatory thalamic neurons. Kim et al., Cell Reports 2025. Note: GEO provides raw nuclei counts only; cell types here were reproduced from the raw data by following the authors' published pipeline and assigned by marker signature per the paper's Figure 7 identities (a derived reproduction, not a deposited annotation).
View DatasetZona Incerta — GABAergic Neurons (snRNA-seq)
Single-nucleus RNA-seq of the adult mouse zona incerta (ZI), NeuN+ FANS-sorted. The ZI is predominantly GABAergic; this dataset resolves its GABAergic neuron populations by the paper's complementary markers — Meis2 (ventral/caudal ZI), Ptprk/Kcng2 (dorsal ZI), and Pax6 — alongside a minority of glutamatergic neurons from adjacent structures (dorsal thalamus, subthalamic nucleus, hypothalamus) and a small glial complement. Kast et al., PNAS 2026. Note: GEO provides raw nuclei counts only; cell types here were reproduced from the raw data and assigned by marker signature per the paper's identities (a derived reproduction, not a deposited annotation).
View DatasetHabenula — MHb & LHb (scRNA-seq, Hashikawa)
Single-cell RNA-seq of the mouse habenular complex (medial and lateral habenula), profiled with Act-seq (immediate-early-gene-suppressed). Resolves glutamatergic MHb neurons (Tac2), the ventral MHb cholinergic subset (Chat/Slc18a3), lateral habenula neurons (Gap43/Htr2c/Pcdh10), and the habenular glia. Like the wider habenula, this dataset is GABA-negative (low Gad2). Hashikawa et al., Neuron 2020. Note: GEO provides raw counts only; cell types here were reproduced from the raw data and assigned by marker signature per the paper's identities (a derived reproduction, not a deposited annotation).
View DatasetHabenula — MHb (scRNA-seq, Caligiuri)
Single-cell RNA-seq of the mouse habenula (medial-habenula-focused), from the saline arm of a wild-type vs Hhip-mutant study. Resolves MHb neurons (Tac2), lateral habenula neurons (Gap43), other glutamatergic habenular neurons, and the surrounding glial, vascular, ependymal and choroid-plexus cells captured in this peri-ventricular dissection. A GABA-negative habenula reference. Caligiuri et al., PNAS 2022. Note: GEO provides raw counts only; cell types here were reproduced from the raw data and assigned by marker signature (a derived reproduction, not a deposited annotation).
View DatasetHabenula — Control snRNA-seq (Minerva)
Single-nucleus RNA-seq of the mouse habenula (control samples, 3 male + 3 female). The habenula is predominantly glutamatergic; this dataset resolves MHb neurons (Tac2), lateral habenula neurons (Gap43/Htr2c/Chrm3), other glutamatergic habenular neurons, a rare GABAergic neuron population, and the habenular glia. A GABA-poor habenula reference. From Minerva et al., Cell Reports 2026 (control habenula subset of a VTA stress study). Note: GEO provides raw counts only; cell types here were reproduced from the raw data and assigned by marker signature (a derived reproduction, not a deposited annotation).
View DatasetHuman DRG — Sensory Neurons (snRNA-seq)
Single-nucleus RNA-seq of adult human dorsal root ganglion (DRG), resolving the transcriptomic classes of human somatosensory neurons. A public human sensory-neuron reference. Nguyen et al., eLife 2021. Hosted as deposited (the authors' own cell-type annotations and embedding are shown unchanged); obtained from CZ CELLxGENE under a CC-BY 4.0 license.
View DatasetHuman Retina — Cell Atlas (scRNA-seq)
Single-cell RNA-seq atlas of the adult human neural retina, resolving the major retinal cell classes (rods, cones, bipolar, amacrine, horizontal, Muller glia, retinal ganglion cells, and others). A compact public human retina reference. Lukowski et al., EMBO J 2019. Hosted as deposited (the authors' own cell-type annotations and embedding shown unchanged); obtained from CZ CELLxGENE under a CC-BY 4.0 license.
View DatasetMouse Nodose (Vagal) Ganglion — NodoMap
Integrated single-cell/single-nucleus RNA-seq atlas of the mouse nodose (inferior vagal) ganglion — the sensory ganglion of the vagus nerve — resolving ~52 neuronal and non-neuronal cell types. A public vagal-sensory reference (NodoMap). Hosted as deposited (the authors' own annotations and embedding shown unchanged); obtained from CZ CELLxGENE under a CC-BY 4.0 license. Source is a 2025 preprint.
View DatasetMouse Retina — Cell Atlas (scRNA-seq)
Unified single-cell RNA-seq atlas of the mouse retina (all cells), resolving the major retinal classes and ~120 fine cell types (rod/cone photoreceptors, bipolar, amacrine, horizontal, Muller glia, retinal ganglion cells, and non-neuronal cells). The mouse companion to human retina atlases. MRCA, iScience 2024. Hosted as deposited (the authors' own annotations and embedding shown unchanged); obtained from CZ CELLxGENE under a CC-BY 4.0 license.
View DatasetMouse Hypothalamus — Unified Atlas (HypoMap)
HypoMap: a unified single-cell gene-expression atlas of the mouse hypothalamus, integrating 17 datasets (384,925 cells) across the preoptic-to-posterior hypothalamic axis (ARC, PVN, VMH, DMH, LHA, POA, SCN and more). The field's reference hypothalamus atlas. Steuernagel et al., Nat Metab 2022. Hosted as deposited (the authors' own curated cell classes and embedding shown unchanged); obtained from CZ CELLxGENE under a CC-BY 4.0 license.
View DatasetMouse Trigeminal Ganglion — iPain Atlas (integrated)
Integrated single-cell atlas of the mouse trigeminal ganglion (84,658 cells) from the iPain resource, combining the authors' own profiling with previously published trigeminal ganglion datasets across 10x, BD Rhapsody, Drop-seq, Smart-seq3 and inDrop. Cells carry the authors' 18 cell-type labels (sensory neuron subtypes and the satellite glia, Schwann, fibroblast, vascular and immune compartments), a 10-class summary, and the deposited condition, time-point, source-study and technology labels. Techameena et al., Nat Commun 2024. Hosted as deposited (the authors' annotations and embedding are shown unchanged); obtained from CZ CELLxGENE Discover under a CC BY 4.0 license.
View DatasetHuman Retina Cell Atlas — scRNA-seq (integrated)
Integrated single-cell RNA-seq atlas of the adult human retina (265,767 cells) from the Human Retina Cell Atlas, combining five published studies across twenty donors, spanning fovea, macula and peripheral retina. Cells carry the authors' 22 cell-type labels covering rod and cone photoreceptors, the bipolar, amacrine and horizontal interneuron types, midget and parasol ganglion cells, Muller glia, astrocytes, microglia and retinal pigment epithelium, with a 10-class summary and the source study, donor, tissue region and assay per cell. Li et al., Nat Genet 2026. Hosted as deposited (the authors' annotations and embedding are shown unchanged); obtained from CZ CELLxGENE Discover under a CC BY 4.0 license.
View DatasetHuman Hypothalamus — HYPOMAP (snRNA-seq)
Single-nucleus RNA-seq atlas of the adult human hypothalamus (433,369 nuclei) from HYPOMAP, integrating the authors' donors with the Siletti et al. human brain atlas hypothalamus nuclei, with the sampled hypothalamic region recorded per nucleus. Nuclei carry the authors' hierarchical cluster names at three levels: 13 classes (astrocytes, ependymal, oligodendrocyte lineage, the GABAergic and glutamatergic neuron branches, vascular and immune cells), 52 cell types and 156 fine types. Tadross et al., Nature 2025. Hosted as deposited (the authors' annotations and embedding are shown unchanged); obtained from CZ CELLxGENE Discover under a CC BY 4.0 license.
View DatasetDRG Neurons Across Species — Mouse, Human, Macaque, Guinea Pig
Cross-species single-cell atlas of dorsal root ganglion sensory neurons (6,608 neurons, balanced across mouse, human, cynomolgus macaque and guinea pig), integrated on a shared gene namespace so the same eleven neuron types can be compared between species. Cells carry the authors' neuron-type labels and their species, and a human-versus-mouse comparison is precomputed per neuron type. Jung et al., Nat Commun 2023. Hosted as deposited (the authors' integration, embedding and labels are shown unchanged); genes are mouse symbols for all four species.
View DatasetInfant KMT2A-rearranged B-ALL — Full Cohort (scRNA-seq)
Single-cell RNA-seq of 128,588 cells from 18 infants (5 days to 11 months) with KMT2A-rearranged B-cell acute lymphoblastic leukemia, spanning six fusion partners (MLL-ENL, MLL-AF4, MLL-AF9, MLL-AF10, MLL-AF1P and t(7;11)(q22;q23)). Leukemic blasts dominate the object (88,228 cells) alongside the residual normal compartment — T/NK, mature B, monocyte, dendritic and progenitor populations. Three annotation lenses are available: a six-way top-level view, the authors' resolved cell types, and a projection of every cell onto normal haematopoiesis ("Pre-pro-B-like", "CLP-like", and so on) that shows how far along the normal B-lineage each blast population sits. Deposited processed object from the HTAN-CHOP collection (Blood 2022); counts, embedding and all annotations are the authors' own.
View DatasetInfant KMT2A-rearranged B-ALL — Immune Compartment (scRNA-seq)
Single-cell RNA-seq of the immune and microenvironment compartment from the same 18 infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia as HTAN_BALL_MAIN, re-embedded without the leukemic blasts to resolve the T and NK compartments in detail. Separates naive, central-memory and effector-memory CD4+ and CD8+ T cells, cytotoxic and exhausted T subsets, NKT and CD56+/CD16+ NK cells, mature B cells, CD14+ and CD16+ monocytes, and conventional and plasmacytoid dendritic cells. Deposited processed object from the HTAN-CHOP collection (Blood 2022); counts, embedding and cell-type annotations are the authors' own.
View DatasetCD19-CAR T Cells in B-ALL — CAR+ vs CAR- (scRNA-seq)
Single-cell RNA-seq of 37,100 CD19-CAR T cells from five patients with B-cell acute lymphoblastic leukemia, comparing CAR-expressing (CAR+) and non-transduced (CAR-) T cells in the infusion product and again at peak in vivo expansion. Resolves naive, central- and effector-memory and cytotoxic CD4+ and CD8+ subsets, gamma-delta T cells, and three distinct proliferating populations (early MCM3/5/7+ PCNA+, and late histone-enriched MKI67+, CCNB1/2+ CDK1+ and STMN1+ BIRC5+). Transduction status, timepoint and clonal expansion category are all available for splitting plots. Deposited processed object; counts, the Harmony-integrated embedding and all annotations are the authors' own.
View DatasetHigh-Risk Neuroblastoma — Diagnosis vs Post-Treatment (scRNA-seq)
Longitudinal single-cell RNA-seq atlas of 372,619 cells from 22 children with high-risk neuroblastoma, sampled at diagnosis and again after induction chemotherapy, across primary adrenal and abdominal tumours and metastatic sites in liver, lymph node, chest and neck. Resolves the malignant neuroblast compartment alongside the tumour microenvironment -- fibroblasts, macrophages, T and B cells, dendritic cells, Schwann cells, endothelium, and adrenal cortical, hepatocyte and kidney cells from the surrounding tissue. Every cell carries the donor's MYCN amplification, ALK and TP53 mutation status, treatment response, relapse event and vital status, so diagnosis-versus- post-treatment and MYCN-amplified-versus-non-amplified comparisons can be made directly in the plotting tools. Deposited processed object from the HTAN CHOP collection; counts, embedding and annotations are the authors' own.
View DatasetAcute Myeloid Leukemia Atlas — 20 Studies, Adult and Paediatric (scRNA-seq)
Integrated single-cell RNA-seq atlas of 748,679 bone marrow and blood cells pooled from 20 published studies of acute myeloid leukemia, spanning 581,914 leukemic cells and 166,765 cells from healthy donors, and 168,384 paediatric alongside 544,126 adult cells. Resolves the haematopoietic hierarchy — HSPC, CMP, GMP and MEP progenitors, promonocytes, CD14+ and CD16+ monocytes, erythroid cells, conventional and plasmacytoid dendritic cells, B, pro-B, plasma, T and NK cells. Every cell carries its source study, ELN risk group (adverse / intermediate / favourable / healthy donor), detected translocation (RUNX1-RUNX1T1, CBFB-MYH11, PML-RARA, BCR-ABL and the MLL fusions), mutation and cytogenetic calls, and a fine-grained progenitor state where the submitters assigned one — so leukemic-versus-normal, adult-versus-paediatric and risk-group comparisons can be made directly in the plotting tools. Deposited processed object; counts, the scVI-integrated embedding and all annotations are the authors' own.
View Dataset