DOI: 10.25452/figshare.plus.29190726
title: Processed data for X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models

description: 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 <b>X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models. </b>This dataset is also available on Hugging Face.Dataset:HCT116:<b>HCT116_filtered_dual_guide_cells.h5ad</b>: HCT116 cells that contain two sgRNAs targeting the same gene and from the same guide pair<b>HCT116_filtered_dual_guide_cells.h5ad.md5</b>: checksum for HCT116_filtered_dual_guide_cells.h5adHEK293T:<b>HEK293T_filtered_dual_guide_cell</b><b>s</b><b>.h5ad</b>: HEK293T cells that contain two sgRNAs targeting the same gene and from the same guide pair<b>HEK293T_filtered_dual_guide_cell</b><b>s</b><b>.h5ad.md5</b>: checksum for HEK293T_filtered_dual_guide_cells.h5adh5ads containing all aligned cells to be released at a later date.Description of h5ads: h5ads are AnnData objects that contain the following metadatacell-level (obs):sample: GEM batchnum_features: number of guidesguide_target: guide identitygene_target: gene targeted by guiden_genes_by_counts: number of genes with non-zero countstotal_counts: total UMIstotal_counts_mt: total UMIs from MT genespct_counts_mt: % UMIs from MT genespass_guide_filter: boolean if cells contains two guides from the same guide pairgene-level (var):mt: boolean if gene is MT genen_cells_by_counts: number of cells gene has non-zero UMIs inmean_counts: mean UMIs over all cellspct_dropout_by_counts: % of cells this gene does not appear intotal_counts: sum of UMIs for a geneOther files:<b>guide_library.csv</b>: Table containing guide pairs in X-Atlas/Orion. Guide sequences are from Replogle, et al. eLife (2022). Description of columns:target_gene: gene symbol of target genetarget_gene_id: Ensembl ID of target geneid_a: unique identifier for the first guide in the pair (Guide A). Used in .obs.guide_targetid_a (Replogle et al): original name of Guide A in Replogle, et al. eLife (2022)sequence_a: sequence of Guide Aid_b: unique identifier for the second guide in the pair (Guide B). Used in .obs.guide_targetid_b (Replogle et al): original name of Guide B in Replogle, et al. eLife (2022)sequence_b: sequence of Guide Bid_ab: unique identifier for guide pair (id_a | id_b)<b>HCT116_filtered_guide_calls_per_cell.csv.gz</b>: Table containing guide UMIs for HCT116 cells that contain two sgRNAs targeting the same gene and from the same guide pair. Description of columns:cell_barcode: 10X-generated cell barcode. the suffix -1 is replaced with -SAMPLEnum_features: number of guides in the cellfeature_call: identities of guides in the cell (Guide A | Guide B)num_umis: numbers of UMIs for each guide (Guide A UMIs | Guide B UMIs)gene_target: gene targeted by guidespass_guide_filter: boolean if cells contains two guides from the same guide pair<b>HEK293T_filtered_guide_calls_per_cell.csv.gz</b>: Table containing guide UMIs for HEK293T cells that contain two sgRNAs targeting the same gene and from the same guide pair. Contains the same columns as HCT116_filtered_guide_calls_per_cell.csv.gz