Next generation sequencing (NGS) technologies have enabled the generation of huge quantities of transcriptomics data using bulk tissue RNA sequencing (RNA-seq) technologies, which has recently developed further to capture gene expression at single cell resolution (scRNA-seq). This has led to detection of cell types and communications, novel gene transcripts, novel regulatory mechanisms, allele specific gene expression and numerous non-coding RNAs (ncRNAs) generating major implications for unravelling biology of cattle health, welfare and production. In this chapter, an overview of the bulk and scRNA-seq technologies and related bioinformatics tools from processing raw reads to final analyses are described. Differential expressions, co-expression networks, machine learning and systems genetics approaches are also elaborated. Case studies in dairy cattle feed-efficiency and Invitro embryo production and transfer technologies are provided, followed by challenges and future trends in transcriptomics, namely multi-omics integration and use of artificial intelligence methods for precision dairy cattle management and breeding.