packer2019.h5ad

<b>Notebook wrangling the data: </b>https://github.com/WormBase/wormcells-notebooks<b><br></b><b>Original study</b>A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution<br>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.<br>Science 20 Sep 2019: Vol. 365, Issue 6459, eaax1971 DOI: 10.1126/science.aax1971 https://science.sciencemag.org/content/365/6459/eaax1971.editor-summary<br><b>Data description and link</b>89,701 cells profiled with 10xv2 across multiple timepoints of development<br>Data available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126954<br><br>print(adata) AnnData object with n_obs × n_vars = 20222 × 89701 obs: 'gene_id', 'gene_name' var: 'barcode', 'n_umi', 'time_point', 'batch', 'size_factor', 'cell_type', 'cell_subtype', 'plot_cell_type', 'raw_embryo_time', 'embryo_time', 'embryo_time_bin', 'raw_embryo_time_bin', 'lineage', 'passed_qc', 'experiment' print(adata.var.head(1).T) AnnData object with n_obs × n_vars = 20222 × 89701 obs: 'gene_id', 'gene_name' var: 'barcode', 'n_umi', 'time_point', 'batch', 'size_factor', 'cell_type', 'cell_subtype', 'plot_cell_type', 'raw_embryo_time', 'embryo_time', 'embryo_time_bin', 'raw_embryo_time_bin', 'lineage', 'passed_qc', 'experiment' print(adata.obs.head(1).T) WBGene00010957 gene_id WBGene00010957 gene_name nduo-6<br>