Skip to content

Example datasets

Descriptions and download links for the datasets used in the Hooke vignettes.

Silica-induced pulmonary fibrosis [mouse]:

Silicosis data (.RDS)

Subclustered and finely annotated whole-lung single-nucleas RNA sequencing from a silica-induced pulmonary fibrosis mouse model.

This studied was published in Hasegawa, Franks, et al. bioRxiv, (2023)

Cell metadata breakdown

Important columns in this data:

  • ID - individual sample ID.
  • Timepoint - timepoint the lung was sampled.
  • Rep - replicate
  • fine_annotation - The finest cell type annotation level.
  • broad_annotation - A broader level of cell type annotation than cell_type_sub, but still capturing all uniquely identified cell types.

Cranial sensory ganglia [zebrafish]:

Subclustered and finely annotated sensory cranial ganglia cells (plus Rohon-Beard neurons). This dataset contains just wild type and control-injected cells.

Cranial ganglia subset (.RDS)

Our findings are published in Saunders, Srivatsan, et al. Nature, in press (2023). For more information about this dataset, see the ZSCAPE website.

Cell metadata breakdown

Our cell metadata contains lots of information about time, perturbation, statistical metrics, and annotation. Here is a breakdown of those attributes according to our column names:

  • timepoint: The developmental stage in hours post fertilization (hpf) of embryos. Embryos were staged according to key landmarks according to (Kimmel, et al (1995)). Options are 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 72, and 96 hpf.
  • expt: Denotes unique library preparation instances.
  • cell_type_sub: The finest cell type annotation level.
  • cell_type_broad: A broader level of cell type annotation than cell_type_sub, but still capturing all uniquely identified cell types.
  • tissue: The tissue type annotation that contains the cell types.
  • germ_layer: The germ layer of origin for each cell type, if known.
  • gene_target: The genetic perturbation target. Controls include injected (scrambled) and unjected. Sibling controls are listed as ctrl-<target>, for null mutants included in the study.
  • mean_nn_time: The mean time points of the nearest 15 neighbor cells
  • embryo: The individual embryo barcode.
  • temp: The growth temperature of the embryos (standard conditions are 28C).
  • pseudostage: Embryo-level staging prediction by cell composition.