Computational protocol: Interference with DNA repair after ionizing radiation by a pyrrole-imidazole polyamide

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Protocol publication

[…] LNCaP and VCaP cells were plated at 5 × 104 cells/mL in 10-cm2 dishes, treated with or without 10 μM 1 in RPMI 1640 and DMEM supplemented with 10% FBS, respectively, for 24 hours. Total RNA was TRIzol extracted, sequenced (Illumina HiSeq2000), and mapped against the human genome (hg19) with Tophat2 using Ensembl GRCh37 gene annotations. Htseq-count was used for exon alignment and DESeq2 for differential expression. Pathway analysis was performed with the gene set enrichment analysis (GSEA) software on genes with padj<0.05 and p<0.05 for LNCaP and VCaP, respectively. […]

Pipeline specifications

Software tools TopHat, HTSeq, DESeq2, GSEA
Application RNA-seq analysis