Cell Atlas

Every cell is one point. Drag to pan, scroll to zoom, shift-drag to select a region; click any group in the legend to isolate it. Use Colour cells by to switch between cell type, cluster, library, quality-control metric and the expression of a single gene.

Cell types in this dataset

Click a cell type to isolate it in the atlas above.

Cell type Cells Percent Markers
Ectoderm 25,986 71.10% marker genes
Secretory Progenitor 2,713 7.42% marker genes
Endoderm 2,055 5.62% marker genes
Unannotated 1,542 4.22% marker genes
Mesoderm 1,489 4.07% marker genes
Cnidocytes 1,471 4.02% marker genes
Neuronal 730 2.00% marker genes
Gland Cells 564 1.54% marker genes

Quality control for this dataset

These are the figures actually applied to the cells shown above, not the values requested in a configuration file. Every dataset is filtered independently; see Single-cell Data for the full table across all datasets.

Source BioProject PRJNA1327231
SRA study SRP619054
GEO series GSE307733
Library type 10x Genomics Chromium (high confidence)
Libraries integrated 7
Cells before filtering 36,568
Cells after cell filtering 36,568
Doublets removed 18 (0.05%)
Cells after filtering 36,550
Retained 100.0%
Filtering strategy Per-library MAD outlier detection (adaptive)
Thresholds applied adaptive: per-library MAD (5.0 MADs) on UMI, genes and MT%, floor 200 genes, floor 500 UMI
Mitochondrial genes found 0 — too few for a reliable MT% filter, so none was applied
Doublet method Scrublet (per library)
Integration method Harmony on sample (7 libraries)
Cell-type annotation Inherited from the source publication
Cell-type labels from GSE307733_g.cell_to_cts.csv.gz (100% of cells matched)
Pipeline version cnidosite-sc-1.0.0
Processed 2026-09-20T03:34:23+00:00
Clusters / cell types 17 / 8
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