Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.
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Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.
A) Excel Workbooks for RNA seq analysis showing the differential expression results for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.
Samples F01_5 and F01_6 represent shRNA NTC PEO-1 and F01_7 to F01_8 represent shRNA PRLR PEO-1.
Sheet 1: statistically significant up-regulated genes with log2fold change of >= 1 (sorted by fold change).
Sheet 2: statistically significant down-regulated genes with log2fold change of <= -1 (sorted by fold change)
Sheet 3: Statistically significant differentially expressed (DE) genes (p value =< 0.05 and p adj =< 0.05) including normalised counts for each sample (rounded values)
Sheet 4: Differential expression analysis results (raw) including normalised counts for each sample.
Sheet 5: Raw counts for the six samples (three replicates PEO-1 shRNA NTC and three replicates PEO-1 shRNA PRLR
Sheet 6: Filtered normalised counts (all genes with row Sum less than one were removed)
The data presented log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic and fold change are included.
B) List of genes in the top up-regulated and down-regulated hallmark pathways, which were affected by PRLR knockdown in PEO-1 cells.
Sheet 1: list of all (raw) hallmark pathways affected by knocking down PRLR generated by set enrichment analysis (GSEA) in R using the Bioconductor package fgsea.
Sheet 2: list of significantly affected pathways with (p value =< 0.05 and p adj =< 0.05)
Sheet 3: list of gene in Myc targets V1 pathway
Sheet 4: list of gene in Myc targets V2 pathway
Sheet 5: list of gene in epithelial mesenchymal transition pathway
Sheet 6: list of gene in glycolysis pathway
Sheet 7: list of gene in oxidative phosphorylation pathway.
The data presented NES= normalised enrichment score, NE= enrichment score, n More Extreme= number of times a random gene set had a more extreme enrichment score value, log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic , fold change, p value, and read count are included.
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