Published May 19, 2021 | Version 1.0
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Ben-David et al 2021 scRNAseq dataset wrangled into standard WormBase anndata- 55k cells profiled with 10xv2 at L2 larval stage

  • 1. ROR icon California Institute of Technology


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 The notebook used to wrangle the data is available at: **Whole-organism eQTL mapping at cellular resolution with single-cell sequencing** _Eyal Ben-David, James Boocock, Longhua Guo, Stefan Zdraljevic, Joshua S Bloom, Leonid Kruglyak_ eLife 2021;10:e65857, DOI: []( ### Data description and links 55,508 cells profiled with 10xv2 on L2 larvae Raw sequencing data is available at The authors kindly provided the original gene count matrix without the soupX modifications, which is used to create the .h5ad file in this notebook. The author provided files are: ``` bendavid2021_barcode_metadata_for.csv bendavid2021_gene_metadata.csv ``` The R object as processed by the authors with soupX is also available on GitHub together with all the code to make the figures and calculate the numbers reported in the paper: [](


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