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Fig. 1 | BMC Genomics

Fig. 1

From: Understanding the regulatory mechanisms of milk production using integrative transcriptomic and proteomic analyses: improving inefficient utilization of crop by-products as forage in dairy industry

Fig. 1

An overview of the transcriptomic and proteomic experiment. Schematic diagram of workflow of the RNA-seq transcriptomic and iTRAQ-based proteomic experiments. Six cows were fed either corn stover (CS) or alfalfa hay (AH) as forage for 14 weeks. RNA from two cows and protein samples from three cows within each group were pooled for transcriptomic (3 replicates/group) and proteomic (2 replicates/group) analyses. For transcriptomic assay, the pooled RNA was sequenced on the Illumina platform, and subsequently the reads were aligned and mapped to the Bos taurus genome. For the proteomic assay, the extracted proteins were digested with trypsin, and the peptides are labeled with different iTRAQ reagents, which contain reporter groups of different masses (114, 115, 116, 117), balance groups of different masses (191, 190, 189, 188), and a reactive group (R). The labeled peptides are then mixed equivalently and fractionated by strong cation exchange (SCX) chromatography. Fractions were separated by liquid chromatography (LC) and analyzed by two-step mass spectrometry (MS)

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