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This dataset (X-Atlas/Orion) contains processed data from two genome-wide Perturb-seq experiments in HCT116 and HEK293T cell lines described in the manuscript X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models
HEK293T: HEK293T_filtered_dual_guide_cells.h5ad: HEK293T cells that contain two sgRNAs targeting the same gene and from the same guide pair HEK293T_filtered_dual_guide_cells.h5ad.md5: checksum for HEK293T_filtered_dual_guide_cells.h5ad h5ads containing all aligned cells to be released at a later date.
Description of h5ads: h5ads are AnnData objects that contain the following metadata
cell-level (obs): sample: GEM batch num_features: number of guides guide_target: guide identity gene_target: gene targeted by guide n_genes_by_counts: number of genes with non-zero counts total_counts: total UMIs total_counts_mt: total UMIs from MT genes pct_counts_mt: % UMIs from MT genes pass_guide_filter: boolean if cells contains two guides from the same guide pair gene-level (var): mt: boolean if gene is MT gene n_cells_by_counts: number of cells gene has non-zero UMIs in mean_counts: mean UMIs over all cells pct_dropout_by_counts: % of cells this gene does not appear in total_counts: sum of UMIs for a gene
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