Packer et al 2019 scRNAseq dataset wrangled into standard WormBase anndata- 89k cells profiled with 10xv2 across multiple timepoints of development

This is part of a curated collection of all C. elegans single cell RNA sequencing high throughput data wrangled into the anndata format in .h5ad files with standard fields, plus any number of optional fields that vary depending on the metadata the authors provide. As possible, we attempt to keep the field names lower case, short, descriptive, and only using valid Python variable names so they may be accessed via the syntax adata.var.field_name For the convention used to wrangle the h5ad files see github.com/WormBase/single-cell/blob/main/data_wrangling_convention.md Notebook used to wrangle the data: github.com/WormBase/wormcells-notebooks/blob/main/wormcells_wrangle_packer2019_h5ad.ipynb Original study: A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution Packer, Jonathan S. and Zhu, Qin and Huynh, Chau and Sivaramakrishnan, Priya and Preston, Elicia and Dueck, Hannah and Stefanik, Derek and Tan, Kai and Trapnell, Cole and Kim, Junhyong and Waterston, Robert H. and Murray, John I. Science 20 Sep 2019: Vol. 365, Issue 6459, eaax1971 DOI: 10.1126/science.aax1971 science.sciencemag.org/content/365/6459/eaax1971.editor-summary Data description: 89,701 cells profiled with 10xv2 across multiple timepoints of development Data available at: ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126954 Fields of the anndata object as printed from Python: ``` print(adata) AnnData object with n_obs × n_vars = 20222 × 89701 obs: 'gene_id', 'gene_name' var: 'study', 'batch', 'sample', 'sample_description', 'barcode', 'cell_type', 'n_umi', 'time_point', 'size_factor', 'cell_subtype', 'plot_cell_type', 'raw_embryo_time', 'embryo_time', 'embryo_time_bin', 'raw_embryo_time_bin', 'lineage', 'passed_qc' print(adata.var.head(1).T) AnnData object with n_obs × n_vars = 20222 × 89701 obs: 'gene_id', 'gene_name' var: 'study', 'batch', 'sample', 'sample_description', 'barcode', 'cell_type', 'n_umi', 'time_point', 'size_factor', 'cell_subtype', 'plot_cell_type', 'raw_embryo_time', 'embryo_time', 'embryo_time_bin', 'raw_embryo_time_bin', 'lineage', 'passed_qc' print(adata.obs.head(1).T) WBGene00010957 gene_id WBGene00010957 gene_name nduo-6 ```