dsRNAiDilutionSeriesData: dsRNA dilution series

In Huber-group-EMBL/RNAinteractMAPK: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi

Description

A dilution series for 6 x 6 gene. For each gene pair all combinations of 8 different concentrations of dsRNA reagent are screened. Three readout channels (nrCells, area, intensity) are available in the data.frame dsRNAiDilutionSeries. The plate annotation is given in the data.frame dsRNAiDilutionSeriesAnno and precomputed degrees of freedom for thin plate splines are available in the matrix dsRNAiDilutionSeriesDF.

Usage

data(dsRNAiDilutionSeries)

Format

• dsRNAiDilutionSeries: A data frame with 2688 observations on the following 3 variables.

  nrCells

  a numeric vector representing the number of cells readout.

  area

  a numeric vector representing the are readout.

  intensity

  a numeric vector representing the intensity readout.

• dsRNAiDilutionSeriesAnno: A data frame with 2688 observations on the following 7 variables.

  plate

  a numeric vector representing the plate number.

  well

  a numeric vector representing the well.

  row

  a numeric vector representing the row on plate.

  col

  a numeric vector representing the column on plate.

  targetID1

  a numeric vector representing the target number of the first reagent (see targets).

  targetID2

  a numeric vector representing the target number of the second reagent (see targets).

  targets

  a data.frame representing the 49 target reagents For each target reagent the gene name and the dsRNAi concentration is given.

• dsRNAiDilutionSeriesDF: A 6 x 6 matrix with degrees of freedom for thin-plate spline regression.

Source

Horn, Sandmann, Fischer, Huber, Boutros, Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi, Nature Methods, 2011, Figure 1abc and Figure S5.

Examples

data(dsRNAiDilutionSeries)
head(dsRNAiDilutionSeries)
head(dsRNAiDilutionSeriesAnno)
head(dsRNAiDilutionSeriesDF)

Huber-group-EMBL/RNAinteractMAPK documentation built on Dec. 31, 2020, 1:01 p.m.