regvelo.datasets.zebrafish_perturb

regvelo.datasets.zebrafish_perturb(file_path='data/zebrafish_nc/perturbseq_all.h5ad')[source]

Load zebrafish neural crest Perturb-seq dataset.

This dataset contains single-cell CRISPR screening (Perturb-seq) data from zebrafish neural crest (NC) cells, comprising 12,393 cells and 27,599 genes across 9 pooled samples. Cells were perturbed with sgRNAs targeting 22 transcription factors — including ETS-family members (fli1a, elk3, erf, etv2, ets1, elf1), pigment regulators (mitfa, tfec, tfeb), and additional NC regulators (nr2f2, nr2f5, rarga, rxraa, smarcc1a, ebf3a) — as well as combinatorial double or triple knockouts. Unperturbed control and negative-control cells are also included.

Cell type annotations span the major stages of NC development:

  • Neural plate border (NPB) progenitors (NPB_hox, NPB_nohox),

  • Migratory NC cells across axial levels (mNC_arch1, mNC_arch2, mNC_head_mesenchymal, mNC_hox34, mNC_nohox, mNC_trunk, mNC_vagal),

  • Differentiating NC cells (dNC_hox34, dNC_nohox),

  • Pigment cell lineages (Pigment, Pigment_1, Pigment_gch2_high), and

  • Mutant populations (Mutant, Mutant_hox23).

The object includes PCA, PHATE, and t-SNE embeddings, as well as imputed latent time and terminal state assignments.

Parameters:

file_path (str | Path) – Path to local dataset. Will download from remote URL if not found.

Return type:

AnnData

Returns:

: Annotated data object of zebrafish NC Perturb-seq cells.