title: RNASeq of Ovis aries: Control Hypothalamus transcriptome characterization
design: RNA library preparation and pair-end sequencing were performed by the Genome Sequencing and Analysis Facility at the University of Texas, Austin. Barcoded libraries (n = 5 per treatment for each tissue) from hypothalamus and pituitary were prepared and sequencing. The read depth for each sample was approximately 100 million reads per sample. The read lengths for both the hypothalamus and pituitary were 91 base pairs. Raw sequences were examined for quality with FastQC (version 0.10.1). The sequences were trimmed using Trimmomatic (version 0.32) using the pair-end mode parameters. TopHat (version 2.0.12) was used to align the processed reads to the Ovis aries v3.1 genome. Bowtie 2 (version 2.2.1) was used to build the index for the reference Ovis aries genome on which the processed reads were aligned. Cufflinks (version 2.2.1) was used to perform alignment corrections, and Cuffmerge was used to assemble primary transcriptomes.  Cuffquant was used to analyze and quantify gene and transcript expression profiles. Gene counts were normalized in Cuffnorm using FPKM