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Overview

This is where the reference atlas v2.0 and Δlmx1b data is hosted.

Study Design

Our studies produced two data sets:

  1. Reference atlas v2.0 - A hierarchically annotated, individually-resolved reference atlas, comprising 1400 individuals and 1.3 million cells over 19 timepoints (from 18-96 hpf).

  2. Δlmx1b - 500k cells from fish receiving genetic perturbations at 18, 24, 36, 48, 60, and 72 hpf, totaling 200 individually barcoded animals (we collected 8 or more embryos per condition/timepoint)

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: The finest cell type annotation level.
  • cell_type_broad: A broader level of annotation than "cell_type_sub", but still capturing all uniquely identified cell types.
  • tissue: The tissue type annotation that contains the cell types.
  • perturbation: The genetic perturbation target. Controls include injected (scrambled) and uninjected. 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_ID: The individual embryo barcode.
  • partition_group: The annotation that splits the reference into 30 sub UMAPs.

Associated software