Replication data for "The effects of Thymus capitatus essential oil topical application on milk quality: a systems biology approach", Skin swabs Dataset

The Replication data for "The effects of Thymus capitatus essential oil topical application on milk quality: a systems biology approach", Skin swabs Dataset contains 64 compressed fastq format files, representing the forward and reverse reads of 32 skin swab samples belonging to the MILKQUA project that were sequenced in the V3-V4 regione of the 16S rRNA gene. Skin swabs were collected by rubbing sterile swabs on the surface of cow udder, aiming to collect the microbial population present on the udder of cows massaged in that site with Thymus capitatus essential oil (TCEO), to unravel its effects on the microbiota. Guidelines to file naming: Cows were identified with the code CT or TR depending on the belonging to the Control or Treated group respectively, followed by an increasing group-dependent numbering. In the cases of two quarters considered on the same animal, the samples were differentiated adding a letter to the ID (A and B). the samples were collected on day 0, 7, 21 and 28, referred as T0, T7, T21 and T28: therefore, samples were named specifying the timepoint followed by the number samples were paired end sequenced, which produced forward and reverse reads, which were identified with R1 and R2 respectively. Example: CT1A_timepoint0_R1.fastq.gz is a sample belonging to control group, cow number 1 quarter A, collected at T0, and this file is the forward read. All files are in fastq format (.fastq) and compressed (.gz).