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"Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq" Replogle et al. 2022 processed Perturb-seq datasets

dataset
posted on 09.06.2022, 04:56 authored by Joseph ReplogleJoseph Replogle, Jonathan Weissman

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): 

  1. K562 genome-scale perturb-seq sampled at day 8 post-transduction (K562_gwps)
  2. K562 essential-scale perturb-seq sampled at day 6 post-transduction (K562_essential)
  3. 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/).

  1. Raw, single-cell expression data for genes expressed at >0.01 UMI per cell (named $pop_raw_singlecell_01.h5ad)
  2. Raw, pseudo-bulk expression data for genes expressed at >0.01 UMI per cell (named $pop_raw_bulk_01.h5ad)
  3. gemgroup Z-normalized single-cell expression data for genes expressed at >0.01 UMI per cell (named $pop_normalized_singlecell_01.h5ad)
  4. 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.

Funding

DARPA HR0011-19-2-0007

Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human Disease

National Human Genome Research Institute

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The role of TMA7 in mitochondrial dysfunction

National Institute of Neurological Disorders and Stroke

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Predictive engineering of cellular transcriptional state

National Institute of General Medical Sciences

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Cancer Center Support Grant

National Cancer Institute

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History

Research Institution(s)

University of California, San Francisco; Whitehead Institute

Contact email

joseph@wi.mit.edu

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