A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology

The altair.zip archive contains the precomputed source data needed toreproduce the figures of the OPS paper using the analysis code inczbiohub-sf/ops-paper-analysis, together with the reference datasets used for target gene panel selection. The analysis repo expects this folder to be available as its data/ directory, and has instructions for download and extraction. Note that this dataset does not contain any raw data. For access to the full imaging and RNA data visit: biohub.ai --------------------------------------------------------------------------------What's in the folder-------------------------------------------------------------------------------- The data splits into three parts: - Top-level .h5ad files -- AnnData objects with perturbation embeddings used across several figures (cell/gene profiles and their PHATE embeddings). - figures/ -- one subfolder per paper figure (figure_1, figure_2, figure_3, figure_5, plus supplementary SI/), each holding the precomputed tables consumed by the matching notebook in the analysis repo. - target_gene_selection/ -- reference datasets and gene panels (public perturbation screens, pathway/complex annotations, and curated gene lists) used to select the target gene panel for the OPS experiments. --------------------------------------------------------------------------------Folder structure-------------------------------------------------------------------------------- paper_v1_analysis/||-- cropseq_svaeplus.h5ad # CROP-seq sVAE+ gene profiles|-- cropseq_svaeplus_embedding_phate.h5ad # CROP-seq sVAE+ PHATE embedding|-- ops_phase_only.h5ad # OPS (phase-only) gene profiles|-- ops_gene_embedding_phate_phase_only.h5ad # OPS (phase-only) PHATE embedding||-- figures/| || |-- figure_1/| | |-- experiment_correlations_sim_matrix.csv| | `-- iss_barcode_freq_correlation_matrix.csv| || |-- figure_2/| | |-- model_comparison_complex_ebi.csv| | `-- model_comparison_distinctiveness.csv| || |-- figure_3/| | |-- combined_reporter_titration.csv| | |-- gene_reporter_distinctiveness_all.csv| | |-- gene_reporter_distinctiveness_livecell.csv| | |-- marker_organelle_metadata.csv| | |-- titration_individual_reporters.csv| | `-- twist1k_pool_CERES.csv| || |-- figure_5/| | |-- celldino_no_phase_distinctiveness.csv| | |-- celldino_no_phase_ebi.csv| | |-- celldino_phase_only_distinctiveness.csv| | |-- celldino_phase_only_ebi.csv| | |-- celldino_phase_titration.csv| | |-- cropseq_clusters_llm_annotated.csv| | |-- cropseq_ebi_map.csv| | |-- EBI_complexes_v1_updated_gene_names.yaml| | |-- GO_Biological_Process_2025.gmt| | |-- GO_Cellular_Component_2025.gmt| | |-- joint_heatmap_gene_filter.csv| | `-- svaeplus_distinctiveness_std_ntc.csv| || `-- SI/| `-- CLE_QC/ # cell-line engineering QC| |-- flow_tubenames_20250813.xlsx| |-- gfp_pos_CER1.xlsx # GFP-positive flow gating, per CER| |-- gfp_pos_CER2.xlsx| |-- gfp_pos_CER2_2.xlsx| |-- gfp_pos_CER2_3.xlsx| |-- gfp_pos_CER3.xlsx| |-- gfp_pos_CER3_2.xlsx| |-- gfp_pos_CER4.xlsx| |-- gfp_pos_CER4_2.xlsx| |-- relgrowth_day1_BODIPY-493-503.csv # relative growth, per dye| |-- relgrowth_day1_Calbryte.csv| |-- relgrowth_day1_CellEvent.csv| |-- relgrowth_day1_CellROX.csv| |-- relgrowth_day1_FeRhoNox.csv| |-- relgrowth_day1_Fluo-4.csv| |-- relgrowth_day1_Glucose Uptake.csv| |-- relgrowth_day1_Liperfluo.csv| |-- relgrowth_day1_Lipi-Deep-red.csv| |-- relgrowth_day1_LysoTracker.csv| |-- relgrowth_day1_MitoView-633.csv| |-- relgrowth_day1_NucleoLIVE.csv| |-- relgrowth_day1_PeroxiSPY650.csv| |-- relgrowth_day1_pHrodo_AM.csv| |-- relgrowth_day1_pHrodo_Dextran.csv| `-- relgrowth_day1_SPY555_FastAct_X.csv|`-- target_gene_selection/ | |-- CTD_genes_pathways.csv.gz # Comparative Toxicogenomics DB |-- GO_Pathways.csv # Gene Ontology pathway annotations |-- protected_list.txt # curated protected/keep genes |-- gene_panel_2024_07_17_exclude_insufficient_gRNA_genes.csv |-- gene_panel_2024_07_17_genes_with_insufficient_gRNA_genes.csv | |-- Adamson_UPR/ | `-- adamson_s1_uprGenes.csv # Adamson et al. UPR gene set | |-- CORUM/ | `-- CorumhumanComplexes.txt # CORUM human protein complexes | |-- Funk_PhateMapping/ | `-- Funk_Cheeseman_Phate_Data.csv # Funk/Cheeseman PHATE mapping data | |-- Ramezani_PERISCOPE/ | |-- A549_plate_level_median_per_feat_sig_genes_1_FDR_compartment_specific_hits.csv | `-- A549_umap_frozen_version.json | `-- Replogle_PerturbSeq/ |-- annotated_embedding_coordinates.csv |-- clustered_mean_gene_expression_figs2-4.csv.gz |-- Replogle_K562_perturbations.csv `-- Replogle_RPE1_perturbations.csv