Project description:Purpose: Perform RNA-seq study on infectious bovine endometrial tissues to reveal important genes and biological pathways regulating uterine physiology following uterine infections Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among infectious vs normal uterine tract groups Conclusions: The study demonstrated that uterine infections altered several genes and pathways related to inflammatory response, immune response, uterine physiology, uterine enviroment and fertility in the intercaruncular region of bovine endometrium.
Project description:<p>The ovaries and uterus are crucial reproductive organs in mammals, and their coordinated development ensures the normal development of sexual maturity and reproductive capacity. This study aimed to comprehensively capture the different physiological stages of the goat's sexual maturation by selecting four specific time points. We collected samples of ovarian and uterine tissues from five female Jining Gray goats at each time point: after birth (D1), 2-month-old (M2), 4-month-old (M4) and 6-month-old (M6). By combining transcriptomic sequencing of 40 samples (including rRNA-depleted RNA-seq libraries with 3607.8 million reads and miRNA-seq libraries with 444.0 million reads) and metabolomics analysis, we investigated the transcriptomic mechanisms involved in reproductive regulation in the ovary and uterus during sexual maturation, as well as the changes in metabolites and their functional potential. Additionally, we analyzed blood hormone indices and uterine tissue sections to examine temporal changes. These datasets will provide a valuable reference for the reproductive regulation of the ovary and uterus, as well as the regulation of metabolites during sexual maturation in goats.</p><p><br></p><p><strong>Uterine data</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS9795' rel='noopener noreferrer' target='_blank'><strong>MTBLS9795</strong></a>.</p><p><strong>Ovarian data</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS9794' rel='noopener noreferrer' target='_blank'><strong>MTBLS9794</strong></a>.</p>
Project description:Purpose: Perform RNA-seq study on short bovine endometrial tissues to reveal important genes and biological pathways related to uterine development and physiology Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among short vs normal uterine tract groups Conclusions: Heifers with short uterine tract had significantly decreased endometrial layers, uterine glands, and altered transcriptomic profiles. The decrease in uterine glands probably resulted in lower uterine secretions necessary to support embryo growth and development. As a result, heifers with short uteri were infertile even when they were bred by fertile bulls.
Project description:MicroRNAs (miRNAs) are a class of small, non-coding RNAs. MiRNAs regulate developmental activity and may be aberrantly expressed in human diseases, including cancer. Expression of miRNAs is tissue or organ specific. Human uterine leiomyomas (ULMs) are the most common neoplasms of women, characterized by the ovarian sex hormone dependence, worse morbidity in black women and genetic heterogeneity. The high incidence of the disease may be associated with developmental defects in uteri. In this study, we examined miRNA expression in 55 ULMs with matched myometrium using spotted microarray platform. Keywords: Disease state analysis
Project description:Comparison of Gene Expression in Uterine Smooth Muscle Tumors (including normal myometrium, benign uterine leiomyoma, malignant uterine and extra-uterine leiomyosarcoma). Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.