This dataset is a label-free quantitation of proteins milk and dry secretions from the end of lactation through day 21 of the dry period using liquid chromatography with tandem mass spectrometry (LC-MS/MS). The data supplied in this article supports the accompanying publication entitled “Characterization of bovine mammary gland dry secretions and their proteome from the end of lactation through day 21 of the dry period”. The Thermo mass spectrometry raw files and MaxQuant files have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset number PXD017837.

Since 1964, the University of Minnesota has selectively bred a Holstein herd to maintain genetically static, unselected Holsteins (UH). Comparison of these UH cows with contemporary Holstein (CH) has demonstrated that the UH cows not only produce less milk but also have fewer health concerns than their CH herdmates. The objective of this study was to determine the effects of Holstein genotype on innate immune response in an experimental intramammary E. coli challenge model. Primiparous UH (n= 5) and CH (n = 7) cows received 430 cfu E. coli strain P4 in 1 quarter. Blood samples were collected at 0, 0.5, 1, 2, 7d relative to E. coli infusion. RNA Sequencing was conducted using the HiSeq 2500 platform (Illumina, San Diego, CA) to generate an average of 46.96 ± 2.67 million 100 bp paired end reads per sample. For more information about this dataset contact: John Lippolis: john.lippolis@usda.gov Hao Ma: hao.ma@usda.gov