GSE128930
RNA seq of tumors derived from irradiated versus sham hosts transplanted with Trp53 null mammary tissue and fed either Control diet versus Caffeic Acid Phenethyl Ester (CAPE) diet.
Irradiated hosts gave rise to significantly more Trp53 null mammary cancers that grew more rapidly than those in sham-irradiated mice and exhibited an immunosuppressive tumor microenvironment . CAPE prevented the effect of host irradiation on tumor growth rate, immune signature and immunosuppression. Overall design: 10 week-old BALB/c mice were transplanted with Trp53 null mammary tissue 3 days after exposure to low doses of ionizing g-radiation radiation.  Over the next 600 days, tumors were collected. In order to test the hypothesis that host irradiation promotes chronic inflammation, radiation-genetic chimera mice were fed chow containing a honeybee-derived compound with anti-inflammatory and immunomodulatory properties, caffeic acid phenethyl ester (CAPE). RNA sequencing was done on ER negative tumors usingTruSeq RNA Sample Preparation Guide Protocol by Illumina® (#15008136 A). Raw sequencing data were received in FASTQ format.  Read mapping was performed using Tophat 2.0.9 against the mm10 human reference genome.  The resulting BAM alignment files were processed using the HTSeq 0.6.1 python framework and respective mm10 GTF gene annotation, obtained from the University of California, Santa Cruz (UCSC) database.  Subsequently, the Bioconductor package DESeq2(3.2) was used to identify differentially expressed genes (DEG).