Data set for transcriptome analysis of pituitary galnd in cattle breeds

Transcriptome data presented in this article is associated with the research article entitled “Single nucleotide polymorphism discovery in bovine pituitary gland using RNA-seq technology” published in PLOS One [1]. Herein, we provide raw and analysed RNA-seq data of pituitary gland tissues from three cattle breeds, viz., Polish-HF, Polish Red and Hereford cattle breeds. Bioinformatics pipelines of high-quality RNA-seq data includes the FastQC tools for quality controls, Trimmomatic cutadapt tools for trimming RNA-seq data, and BWA version 0.7.5-r404 for mapping and alignment to the Bos taurus reference genome, SAMtools for SNPs identifications in bovine pituitary gland transcriptome. Raw FASTq files for the RNA-seq libraries of bovine pituitary gland were deposited in the NCBI Sequence Read Archive (SRA) and have been assigned BioProject accession PRJNA312148

Data set for transcriptome analysis of liver in cattle breeds

Transcriptome analysis using high-throughput next-generation sequencing (HT-NGS) technology provides the capability to understand global gene expression variations through a wide range of tissue samples in domesticated animals. We provide raw and analysed data for transcriptomic analysis of liver tissues from Polish-HF, Polish Red and Hereford cattle breeds, obtained by RNA-seq. High-quality sequencing data have been analysed using our bioinformatics pipeline which consists of FastQC for quality controls, Trimmomatic for trimming, and BWA version 0.7.5-r404 for alignment to the Bos taurus reference genome, SAMtools for SNPs identifications, and differentially expressed genes (DEGs) identification using DEseq and edgeR pipelines after adjustment for false-discovery rate (FDR) with adjusted two-sided p values <0.01 and the trimmed mean of M values (TMM) normalisation method. The data accompanying the published manuscript describing the SNPs and DEGs identification in the bovine liver transcriptome of cattle breeds. Raw FASTq files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA) and have been assigned BioProject accession PRJNA312148. Raw and processed RNA-seq data were deposited and made publicly available on the Gene Expression Omnibus (GEO; GSE114233)

Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy

During the early stages of pregnancy, the uterine endometrium undergoes dramatic morphologic and functional changes accompanied with dynamic variation in gene expression. Pregnancy-stage specific differentially expressed gene (DEG)-transcript-probes were investigated and identified by comparing endometrium transcriptome at 9th day (9D), 12th day (12D) and 16th day (16D) of early pregnancy in Polish large-white (PLW) gilts. Endometrium comparisons between 9D-vs-12D, 9D-vs-16D and 12D-vs-16D of early pregnancy identified 6049, 374 and 6034 highly significant DEG-transcript-probes (p 2 FC). GO term enrichment analysis identified commonly shared upregulated endometrial DEG-transcript-probes (p 2 FC), that were regulating the gene functions of anatomic structure development and transport (TG), DNA-binding and methyltransferase activity (ZBTB2), ion-binding and kinase activity (CKM), cell proliferation and apoptosis activity (IL1B). Downregulated DEG-transcript-probes (p 2 FC) were involved in regulating the gene functions of phosphatase activity (PTPN11), TC616413 gene-transcript and Susscrofa LOC100525539. Moreover, blastn comparison of microarray-probes sequences against susscrofa11 assembly identified commonly shared upregulated endometrial DEG-transcript-probes (E 2 FC), that were regulating the gene functions of reproduction and growth (SELENOP), cytoskeleton organization and kinase activity (CDC42BPA), phosphatase activity (MINPP1), enzymebinding and cell-population proliferation (VAV3), cancer-susceptibility candidate gene (CASC4), cytoskeletal protein-binding (COBLL1), ion-binding, enzyme regulator activity (ACAP2) Downregulated endometrial DEG-transcript-probes (E 2FC) were involved in regulating the gene functions of signal-transduction (TMEM33), catabolic and metabolic processes (KLHL15). Microarray validation experiment on selected candidate genes showed complementarity to significant endometrial DEG-transcript-probes responsible for the regulation of immune response (IL1B, S100A11), lipid metabolism (FABP3, PPARG), cell-adhesion (ITGAV), angiogenesis (IL1B), intercellular transmission (NMB), cell-adhesion (OPN) and response to stimuli (RBP4) was confirmed by RT-PCR. This study provides a clue that identified pregnancy-stage specific microarray transcript probes could be considered as candidate genes for recognition and establishment of early pregnancy in the pig.</p