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)

Quality control assessment of the RNA-Seq data generated from liver and pituitary transcriptome of Hereford bulls using StrandNGS software

Background: Quality control (QC) assessment is the most critical step in the high-throughput RNA-seq data analysis to characterize the in-depth understanding of genome and transcriptome assembling to a given reference genome. It provides not only a quick insight into the RNA-seq data quality to allow early identification of good or bad RNA-seq data samples, but also to verify the alignment QC checks for further essential high-throughput bioinformatics analysis such as, identification of novel genetic variants, differentially expressed genes (DEGs), gene network and metabolic pathways.Method: After isolation of total RNA from liver (n=15) and pituitary gland (n=15) tissues of young Hereford bulls, the pooled total RNA (n=30) were fragmented using GeneRead rRNA depletion kit (Qiagen, Hilden, Germany) and cDNA library preparation were preformed using ScriptSeqTM v2 RNA-Seq library preparation kit (Epicentre, illumina, USA), followed by high-throughput sequencing of combined liver and pituitary transcriptome using MiSeq reagent kit v2 (illumina, USA) to obtain high quality of paired-end RNA-seq reads of 251 base-pairs (bps). In this paper, the QC assessment of obtained RNA-seq raw data as well as post-alignment QC of processed RNA-seq data of combined liver and pituitary transcriptome (n=30) of Hereford bulls were performed using the strand NGS software v1.3 (Agilent; http://www.strand-ngs.com/) data analysis package. The reads were aligned with Bowtie using default settings against both Bull and Cow genome assembly.Results: Using two runs of MiSeq platform, a total of over 60 million paired-end RNA-seq reads were successfully obtained and submitted to NCBI SRA resources (https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=312148). Library complexity plot results revealed 72.02% of duplicate reads with a low library complexity value of 0.28. The pre-alignment QC analysis of raw RNA-seq data revealed the sequence read lengths ranged from 35-251 bp size with more than 50% of all reads with length over 200bp and 10% of reads below 100bp.Conclusion: By testing the RNA-seq methodology on Illumina platform, two MiSeq sequencing runs yielded significantly high quality of 30 million sequencing reads per single MiSeq run. Our initial pre-alignment and post-alignment analysis of RNA-seq data analysis revealed that mapping of the Hereford liver and pituitary gland transcriptome to reference Bos taurus genome was successfully performed, however, more than 50% of all reads with length over 200bp were recovered. Therefore, obtained results concludes that liver and pituitary transcriptome sequencing with rRNA depletion method is less effective than mRNA RNA-seq method

RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs

BackgroundSingle nucleotide polymorphisms (SNPs) are the well-known molecular markers in genetics and breeding studies applied to veterinary sciences and livestock production. Advancement of next generation sequencing (NGS) provides a high-throughput means of potential putative SNP discovery. The aim of the study was to identify the putative genetic variants in gluteus medius muscle transcriptome of Polish Landrace pigs.MethodsRNA-seq based NGS experiment was performed on Polish Landrace pigs fed with omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) and normal diets. Isolation of total RNA from gluteus medius muscle was performed on low PUFAs (n=6) and High PUFAs dietary group of Polish Landrace pigs. The RNA-seq libraries were constructed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control of raw RNA-seq data was performed using the Trimmomatic and FastQC tools. High QC paired-end RNA-seq data of gluteus medius muscle transcriptome were mapped to the reference genome Sus scrofa v.10.2. Finally, the SNPs discovery was performed using GATK and SAMtools bioinformatics SNPs caller tools.ResultsThe Fastq RNA-seq data generated from two pooled paired-end libraries (151bp) of gluteus medius muscle tissue of Polish Landrace pigs were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Study identified a total of 50.5 million paired-end reads (32.5 million low PUFAs dietary group and 18 million reads high PUFAs dietary group) of gluteus medius muscle transcriptome of Polish Landrace pigs. SNP discovery identified a total of 35436 homozygous and 28644 heterozygous cSNPs in gluteus medius muscle transcriptomes representing both dietary groups of Polish Landrace pig. Moreover, a total of 25187 and 5488 cSNP were identified as synonymous SNPs, and 18005 and 4780 cSNP were identified as nonsynonymous SNPs. Finally, single nucleotide variation (SNV) representing substitutions of all four possibilities (A,T,G,C) were identified ranging 2935 to 3227 SNVs (high PUFAs) and 3528 to 3882 SNVs (low PUFAs) for the heterozygous cSNPs and 2712 to 4058 (high PUFAs) and 4169 to 5692 SNVs (low PUFAs) for the heterozygous SNPs in gluteus medius muscle transcriptomes of Polish Landrace pigs.ConclusionsStudy concluded that identification of cSNPs dataset representing the gluteus medius muscle transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland

RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

Background: RNA-seq technology is most commonly used in quantitative measurement of gene expression levels and identification of non-annotated transcripts. It is also used for the coding SNPs (cSNPs) discoveries in an efficient and cost-effective way. The aim of this study was to identify the putative genetic cSNPs variants in liver transcriptome of Polish Landrace pigs fed with high and low (normal) omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) diets.Methods: RNA-seq based NGS experiment was performed on Polish Landrace pigs fed with high and low PUFAs diets. Total RNA were isolated from liver tissues of low PUFAs (n=6) and high PUFAs dietary group (n=6) of Polish Landrace pigs. The RNA-seq libraries preparations were performed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control (QC) of raw RNA-seq data of liver transcriptome was performed using the Trimmomatic and FastQC tools. The paired-end mapping of the liver transcriptome RNA-seq data (n=12) was performed on the reference genome Sus scrofa v.10.2, followed by cSNPs discovery using GATK and SAMtools bioinformatics SNPs caller tools.Results: Two pooled paired-end libraries of 151bp liver transcriptome of Polish Landrace pigs were generated from MiSeq instrument and subsequent Fastq RNA-seq data were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Our study identified 25.3 million paired-end reads: representing 13,509,248 paired-end reads of high PUFAs dietary group and 11,815,696 paired-end reads of low PUFAs dietary group of Polish Landrace pigs liver transcriptome. The SNP discovery results revealed identification of 25909 homozygous and 23290 heterozygous cSNPs in the liver transcriptome of both dietary groups of Polish Landrace pigs. With regards to same or alternative SNPs alleles encoding amino acids regions, a total of 27141 synonymous cSNP and 5989 non-synonymous cSNPs were identified in liver transcriptome representing high PUFAs dietary group. However, a total of 15128 synonymous cSNPs and 3900 non-synonymous cSNPs were identified in liver transcriptome representing low PUFAs dietary groups of Polish Landrace pigs. The identification of single nucleotide variations (SNVs) representing substitutions of all four possibilities (A,T,G,C) were ranged 2872 to 6868 SNVs (high PUFAs) and 2574 to 3654 SNVs (low PUFAs) in the homozygous cSNPs and 2452 to 2678 SNVs (high PUFAs) and 2094 to 2230 SNVs (low PUFAs) in the heterozygous cSNPs of liver transcriptomes of Polish Landrace pigs, respectively.Conclusions: Study concluded that identification of cSNPs dataset representing the liver transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers for trait-associated studies (viz., growth and metabolic traits) specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in the genetic improvement of the pig production traits using the genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland

Metabolomic Insight into Polycystic Ovary Syndrome—An Overview

Searching for the mechanisms of the polycystic ovary syndrome (PCOS) pathophysiology has become a crucial aspect of research performed in the last decades. However, the pathogenesis of this complex and heterogeneous endocrinopathy remains unknown. Thus, there is a need to investigate the metabolic pathways, which could be involved in the pathophysiology of PCOS and to find the metabolic markers of this disorder. The application of metabolomics gives a promising insight into the research on PCOS. It is a valuable and rapidly expanding tool, enabling the discovery of novel metabolites, which may be the potential biomarkers of several metabolic and endocrine disorders. The utilization of this approach could also improve the process of diagnosis and therefore, make treatment more effective. This review article aims to summarize actual and meaningful metabolomic studies in PCOS and point to the potential biomarkers detected in serum, urine, and follicular fluid of the affected women

Citric Acid as a Potential Prostate Cancer Biomarker Determined in Various Biological Samples

Despite numerous studies, the molecular mechanism of prostate cancer development is still unknown. Recent investigations indicated that citric acid and lipids—with a special emphasis on fatty acids, steroids and hormones (ex. prolactin)—play a significant role in prostate cancer development and progression. However, citric acid is assumed to be a potential biomarker of prostate cancer, due to which, the diagnosis at an early stage of the disease could be possible. For this reason, the main goal of this study is to determine the citric acid concentration in three different matrices. To the best of our knowledge, this is the first time for citric acid to be determined in three different matrices (tissue, urine and blood). Samples were collected from patients diagnosed with prostate cancer and from a selected control group (individuals with benign prostatic hyperplasia). The analyses were performed using the rapid fluorometric test. The obtained results were correlated with both the histopathological data (the Gleason scale as well as the Classification of Malignant Tumors (pTNM) staging scale) and the biochemical data (the values of the following factors: prostate specific antigen, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglyceride, total cholesterol, creatinine and prolactin) using chemometric methods. For tissue samples, the results indicated a decreased level of citric acid in the case of prostate cancer. The analyte average concentrations in serum and urine appeared to be corresponding and superior in the positive cohort. This trend was statistically significant in the case of urinary citric acid. Moreover, a significant negative correlation was demonstrated between the concentration of citric acid and the tumor stage. A negative correlation between the total cholesterol and high-density lipoprotein and prolactin was particularly prominent in cancer cases. Conversely, a negative association between low-density lipoprotein and prolactin levels was observed solely in the control group. On the basis of the results, one may assume the influence of hormones, particularly prolactin, on the development of prostate cancer. The present research allowed us to verify the possibility of using citric acid as a potential biomarker for prostate cancer

Application of laser desorption/ionization techniques in the identification of lipids as prostate cancer biomarkers

Mass spectroscopy has grown enormously over the past century and its variations are used in many fields. One of the methods used to ionize particles is to irradiate the sample with laser radiation. This methods are called laser desorption/ionization techniques and they have great potential for diagnostic applications. Thanks to the so-called soft ionization, direct analysis of a wide variety of compound classes can be used for rapid profiling. Lipids are a diverse group of metabolites that share a common feature of having a hydrophobic fragment. They play an important role in various cellular processes. Changes in lipidome correlate with the symptoms of various diseases. The observation of abnormalities in lipid metabolism is especially important in cancers diagnosed in many patients - such as prostate cancer. Monitoring the level of key biomarkers in the development of a given disease will allow for an earlier correct diagnosis and the use of individual treatment. This short review presents the issues of prostate cancer and the applicability of laser desorption/ionization techniques to identify lipid biomarkers that can be used for rapid identification

In Vivo Efficacy of Wound Healing under External (Bio)AgNCs Treatment: Localization Case Study in Liver and Blood Tissue

The present study reports on the in vivo application of (Bio)silver nanocomposite formulations (LBPC-AgNCs) on wound healing. Additionally, the present study emphasizes the limited uptake of silver by liver and blood tissues as well as the high viability of PBMCs following external LBPC-AgNCs treatment. The wound closure was monitored via stereoscopic microscope, a localization case study in liver and blood tissue was carried out by (Inductively Coupled Plasma–Mass Spectrometers (ICP/MS), and peripheral blood mononuclear cells (PMBC) viability was determined via flow cytometry technique. The silver formulation was applied externally on the site of the wound infection for a period of ten days. At the beginning of the experiment, a moderate decrease in body weight and atypical behavior was observed. However, during the last period of the experiment, no abnormal mouse behaviors were noticed. The wound-healing process took place in a gradual manner, presenting the regeneration effect at around 30% from the fourth day. From the seventh day, the wounds treated with the silver formulation showed 80% of the wound healing potential. The viability of PBMCs was found to be 97%, whereas the concentrations of silver in the liver and blood samples were determined to be 0.022 µg/g and 9.3 µg/g, respectively. Furthermore, the present report becomes a pilot study in transferring from in vitro to in vivo scale (e.g., medical field application) once LBPC-AgNCs have demonstrated a unique wound healing potential as well as a non-toxic effect on the liver and blood