Smart-seq II Sequencing Analysis of Pdl1+ and Pdl1- mammary gland basal cell Transcriptomes

Purpose:Smart sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare gene expression of Pdl1+ and Pdl1- mammary gland basal cell analysis.Methods:Pdl1+ and Pdl1- mammary gland basal cell mRNA profiles of wild-type (WT) were generated by deep sequencing, in triplicate, using Illumina nova seq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Hisat2 as the mapping tool followed byDESeq R package. qRT–PCR validation was performed using TaqMan and SYBR Green assays.Results: Using an optimized data analysis workflow, RNA-seq data confirmed and validated with qRT–PCR. Overall design: Pdl1+ and Pdl1- mammary gland basal cell mRNA profiles of 8 weeks old wild type mice