The first dataset consists of nine gene perturbations with matched control samples (Almudevar et al., 2011 ); the second dataset is composed of two cell types and three treatments (Sampson et al., 2013 (link)); the third dataset is a study of the effect of p53 and/or Ras mutations on gene expression (McMurray et al., 2008 (link)).
In the first dataset, cells transformed to malignancy by mutant p53 and activated Ras are perturbed with the aim of restoring gene expression to levels found in non-transformed parental cells via retrovirus-mediated re-expression of corresponding cDNAs or shRNA-dependent stable knock-down. The data contain four to six replicates for each perturbation, and each perturbation has a corresponding control sample in which only the vector has been added (Almudevar et al., 2011 ).
The second dataset consists of two cell types—young adult mouse colon (YAMC) cells and mutant-p53/activated-Ras transformed YAMC cells—in combination with three treatments—untreated, sodium butyrate or valproic acid. Four replicates were performed for each cell-type/treatment combination (Sampson et al., 2013 (link)).
The third dataset is a comparison between four cell types—YAMC cells, mutant-p53 YAMC cells, activated-Ras YAMC cells and p53/Ras double mutant YAMC cells. Three replicates were performed for the untransformed YAMC cells, and four replicates were performed for each of the other cell types (McMurray et al., 2008 (link)).
As in the original publications, all three datasets were normalized to a reference gene, Becn1, with the resulting values denoted as ΔCt. In the first dataset, ΔΔCt values were computed by comparing each perturbed sample to its corresponding control sample. Additional details regarding each of these datasets can be found in the original publications.
In the first dataset, cells transformed to malignancy by mutant p53 and activated Ras are perturbed with the aim of restoring gene expression to levels found in non-transformed parental cells via retrovirus-mediated re-expression of corresponding cDNAs or shRNA-dependent stable knock-down. The data contain four to six replicates for each perturbation, and each perturbation has a corresponding control sample in which only the vector has been added (Almudevar et al., 2011 ).
The second dataset consists of two cell types—young adult mouse colon (YAMC) cells and mutant-p53/activated-Ras transformed YAMC cells—in combination with three treatments—untreated, sodium butyrate or valproic acid. Four replicates were performed for each cell-type/treatment combination (Sampson et al., 2013 (link)).
The third dataset is a comparison between four cell types—YAMC cells, mutant-p53 YAMC cells, activated-Ras YAMC cells and p53/Ras double mutant YAMC cells. Three replicates were performed for the untransformed YAMC cells, and four replicates were performed for each of the other cell types (McMurray et al., 2008 (link)).
As in the original publications, all three datasets were normalized to a reference gene, Becn1, with the resulting values denoted as ΔCt. In the first dataset, ΔΔCt values were computed by comparing each perturbed sample to its corresponding control sample. Additional details regarding each of these datasets can be found in the original publications.