THP-1 Yao reference data for CRISPR power analysis

Pre-computed pilot data from THP-1 monocytic leukemia cells generated using 10x Chromium technology. Contains baseline gene expression parameters and library size information for power analysis of CRISPR-based perturbation experiments.

Usage

THP1_Yao

Format

A list with 3 elements:

baseline_expression_stats

Data frame with gene expression data (16,373 genes × 3 columns):

• response_id: Character vector of Ensembl gene IDs

• relative_expression: Numeric vector of relative expression levels (TPM/1e6 scale)

• expression_size: Numeric vector of dispersion parameters (theta)

library_parameters

List containing:

• UMI_per_cell: Maximum UMI per cell parameter (77,799)

• variation: Variation parameter for PCR bias (0.354)

mapping_efficiency

Numeric. Mapping efficiency value (0.677)

Source

Paper: Scalable genetic screening for regulatory circuits using compressed Perturb-seq

Author and Year: Yao et al., 2023

Journal: Nature Biotechnology

Accession: GSE221321

PMID: 36747806

Details

This dataset was generated from THP-1 monocytic leukemia cells using single-cell RNA sequencing with 10x Chromium technology.

Cells Used in Relative Expression Estimate: NT (non-targeting) cells in low-moi condition

See also

get_pilot_data_from_package for accessing this data programmatically

Examples

data(THP1_Yao)
str(THP1_Yao)
#> List of 3
#>  $ baseline_expression_stats:'data.frame':	16373 obs. of  3 variables:
#>   ..$ response_id        : chr [1:16373] "ENSG00000238009" "ENSG00000225880" "ENSG00000230368" "ENSG00000224969" ...
#>   ..$ relative_expression: num [1:16373] 1.84e-07 1.49e-06 1.26e-06 5.81e-06 4.16e-06 ...
#>   ..$ expression_size    : num [1:16373] 293.372 422.253 420.589 0.604 0.193 ...
#>  $ library_parameters       :List of 2
#>   ..$ UMI_per_cell: num 77799
#>   ..$ variation   : num 0.354
#>  $ mapping_efficiency       : num 0.677