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
Neural 1 3,348 28.51% marker genes
Secretory 2,054 17.49% marker genes
Gastrodermis 1,760 14.99% marker genes
Progenitor 904 7.70% marker genes
Epidermis 780 6.64% marker genes
Neural 2 723 6.16% marker genes
Neural 4 486 4.14% marker genes
Secretory - Mucous cells 447 3.81% marker genes
Neural 3 351 2.99% marker genes
Undetermined 319 2.72% marker genes
Developing cnidocytes 300 2.55% marker genes
Neural 0 153 1.30% marker genes
Muscle 117 1.00% 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 PRJNA1217498
SRA study SRP560807
GEO series GSE288441
Library type unknown (low confidence)
Libraries integrated 1
Cells before filtering 12,352
Cells after cell filtering 11,742
Doublets removed 0 (0.00%)
Cells after filtering 11,742
Retained 95.1%
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 none (single library)
Cell-type annotation Inherited from the source publication
Cell-type labels from GSE288441_bodywall.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 45 / 13
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