| 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 |