"Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq" Replogle et al. 2022 processed Perturb-seq datasets
This dataset includes data from three Perturb-seq experiments described in Replogle et al. 2022 (https://doi.org/10.1016/j.cell.2022.05.013):
- K562 genome-scale perturb-seq sampled at day 8 post-transduction (K562_gwps)
- K562 essential-scale perturb-seq sampled at day 6 post-transduction (K562_essential)
- RPE1 essential-scale perturb-seq sampled at day 7 post-transduction (rpe1)
For each dataset, there are four processed Perturb-seq files in AnnData format (https://anndata.readthedocs.io/en/latest/).
- Raw, single-cell expression data for genes expressed at >0.01 UMI per cell (named $pop_raw_singlecell_01.h5ad)
- Raw, pseudo-bulk expression data for genes expressed at >0.01 UMI per cell (named $pop_raw_bulk_01.h5ad)
- gemgroup Z-normalized single-cell expression data for genes expressed at >0.01 UMI per cell (named $pop_normalized_singlecell_01.h5ad)
- gemgroup Z-normalized pseudo-bulk expression data for genes expressed at >0.01 UMI per cell (named $pop_normalized_bulk_01.h5ad)
In the anndata format, the .var annotation details genes while the .obs annotation details single-cells/pseudobulk populations.
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Research Institution(s)University of California, San Francisco; Whitehead Institute
Associated Preprint DOI
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