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K562 Gasperini reference data for CRISPR power analysis

K562_Gasperini.Rd

Pre-computed pilot data from K562 chronic myelogenous 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

K562_Gasperini

Format

A list with 3 elements:

baseline_expression_stats

Data frame with gene expression data (19,942 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 saturation curve parameters estimated using preseqR. Data-adaptively selected method: ZTNB. Contains:

  • method_used: "ZTNB" - Zero-truncated negative binomial method

  • L: 4.68e8 - Total expected distinct UMIs at saturation

  • size: 2.14 - ZTNB shape parameter

  • mu: 0.395 - ZTNB mean parameter

  • reads_norm: 23,835 - Normalization constant (reads per cell)

  • n_cells: 7,749 - Number of cells in pilot data

  • UMI_per_cell_at_saturation: 60,414 - Maximum UMI per cell at infinite sequencing depth

mapping_efficiency

Numeric. Mapping efficiency value (0.711)

Source

Paper: A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Author and Year: Gasperini et al., 2019

Journal: Cell

Accession: GSE120861

PMID: 30612741

Details

This dataset was generated from K562 chronic myelogenous leukemia cells using single-cell RNA sequencing with 10x Chromium technology.

Cells Used in Relative Expression Estimate: All cells in high-moi condition

See also

get_pilot_data_from_package for accessing this data programmatically

Examples

data(K562_Gasperini)
str(K562_Gasperini)
#> List of 3
#>  $ baseline_expression_stats:'data.frame':	19942 obs. of  3 variables:
#>   ..$ response_id        : chr [1:19942] "ENSG00000243485" "ENSG00000238009" "ENSG00000241860" "ENSG00000286448" ...
#>   ..$ relative_expression: num [1:19942] 1.50e-07 1.55e-06 7.33e-07 9.31e-07 7.43e-06 ...
#>   ..$ expression_size    : num [1:19942] 0.3556 2.4156 7.7329 0.0341 3.4513 ...
#>  $ library_parameters       :List of 7
#>   ..$ method_used               : chr "ZTNB"
#>   ..$ L                         : num 4.68e+08
#>   ..$ size                      : num 2.14
#>   ..$ mu                        : num 0.395
#>   ..$ reads_norm                : num 23835
#>   ..$ n_cells                   : num 7749
#>   ..$ UMI_per_cell_at_saturation: num 60414
#>  $ mapping_efficiency       : num 0.711