GSE158854
RNA Expression Profiling Comparing ER+ Postpartum Breast Cancer with ER+ Nulliparous Breast Cancer
Purpose: To perform RNA-Seq expression profiling from Young Women's Breast Cancer FFPE tissues, comparing ER+ Postpartum Brest Cancer to ER+ Nulliparous Breast Cancer Methods:  RNA was extracted and isolated from archival Estrogen Receptor Positive primary breast cancer FFPE tissues ( 9 Postpartum, 7 Nulliparous). RNA species selected for inclusion in library utilzing Illumina-Access bead based oligo library preparation representing > 98% of known protein coding genes. Results: We identified gene pathway differences in estrogen receptor signaling, t-cell immunity and cell cycle between nulliparous and postpartum breast cancer cases.  Subset analysis also revealed an enrichment in  extra-cellular matrix pathway related genes in postpartum compared to nulliparous and luminal A cases. Overall design: FFPE derived mRNA from 9 Postpartum  and 7 Nulliparous Young Women's Breast Cancer cases generated by 100-cycle, single-ended, sequencing  of approxinately 70 million reads per sample using Illumina HiSeq 2500 sequencer.  Base call files were converted to fastq format using Bcl2Fastq.