The approach is not only highly sensitive and efficient for identifying differentially expressed genes but, when combined with genomic and genetic analysis can also be used for detecting SNPs in transcribed genes that co-locate with a target locus. These features of RNA-seq analysis are particularly attractive for applications in hexaploid wheat where multiple homoeologous alleles exist for most genes and transcripts. We thus conducted an RNA-seq analysis against five sets of the NILs developed for the Qcrs-3B locus, examined DEGs and SNPs between the NIL lines. This analysis provides candidate genes for both the response determined by the 3BL locus as well as those co-located with the 3BL locus that may be genetically causative for resistance. In addition to identifying genes underlying the FCR resistance locus, we were also interested in finding out if expressed genes associated with resistance to FCR were related to those observed by others for FHB. RNA-seq analysis was conducted against five sets of NILs for a large-effect locus conferring FCR resistance on chromosome arm 3BL in wheat. Not unexpectedly, the numbers of detected SNPEGs from these NILs on the targeted chromosome 3B were significantly higher compared with those on any other chromosome and a large proportion of them were concentrated on the distal end of chromosome arm 3BL where the targeted Qcrs-3B locus locates. Interestingly, this was also observed for DEGs between ‘R’ and ‘S’ isolines suggesting that there may be a regulation of proximally located genes by the Qcrs-3B locus. The use of the multiple sets of NILs allowed the identification of better defined sets of candidate genes underlying the targeted locus. Functions of these genes provide insights into responses regulated by the 3BL locus and the 48 genes mapped in the targeted QTL interval are tractable in further efforts to functionally test gene underlying this QTL for causal effects. These genes are being used as markers in fine mapping the Qcrs-3B locus based on a NILderived population. Gene expression profiling in peripheral blood is frequently performed to identify susceptibility genes or biomarkers for human traits or diseases. Upon collection, RNA profiles change within minutes. Therefore, PAXgene and Tempus Blood RNA Tubes, which allow instant preservation of RNA, are widely used. The suppliers of both types of tubes offer corresponding RNA extraction kits as well as reagents for Y-27632 dihydrochloride downstream applications such as reverse transcription and quantitative real time -PCR assays for quantification of target transcripts. Whereas older extraction kits were optimized for isolation of mRNA, more recent assays were designed to also efficiently extract miRNAs. In the meantime, additional suppliers have launched extraction kits for PAXgene and Tempus Blood RNA Tubes, which are also optimized for parallel mRNA and small RNA extraction. Extraction methods vary depending on the manufacturer and are either based on silica-membranes or magnetic beads. Whereas previous work has investigated quantity and quality of RNA isolated by kits using the same extraction principle from different preservation tubes, comparison of more recently available extraction kits.