Expressed genes in the hypothalamus of gilts cyclic and in anestrus.

Database containing expressed genes in the hypothalamus of sows cyclic and in anestrus. The total RNA of hypophysis of 7 cyclic and 7 gilts was extracted using Trizol (Life Technologie), followed by an RNA cleanup step using the RNeasy mini kit (Qiagen). RNA purity and concentration were measured using Biodrop spectrophotometer (Biodrop) and integrity was evaluated using Bioanalyzer 2100 (Agilent), considering samples with RIN > 7.5 for further analysis. The Illumina Stranded mRNA Prep Kit using 1 μg of total RNA was used for library preparation. After pooling the libraries, clustering, and sequencing were performed in the Illumina NextSeq 2000 sequencer (lllumina) producing 2x150bp paired-end reads, LaCTAD. To perform the RNA-seq analysis BAQCOM, an automated pipeline was used for quality control (QC) and mapping analysis. In this pipeline, Trimmomatic v0.39 was used to filter low-quality reads (QPhred ≤ 20), short reads (< 100bp), and Illumina sequence adapters. Once QC was performed, sequence reads of each sample were mapped against the reference pig genome (Sscrofa11.1, Ensembl release 110) using STAR. Reads counting was performed with HTseq-count and RSEM, which also generated a gene and transcript count table, respectively, for statistical analysis. The differentially expressed (DE) genes, transcripts, and the heatmap were obtained using the limma package from the R 4.2.2 software. The false discovery rate (FDR) which uses the Benjamini-Hochberg (BH) correction for multiple tests was applied and genes and transcripts with ≤ 0.05 were considered DE. Negative and positive fold changes indicate downregulation and upregulation of the genes in the anestrus (affected) compared to the cyclic (control) group.