Uterine infection-induced transcriptomic changes in the bovine endometrium. Uterine infection-induced transcriptomic changes in the bovine endometrium

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. Overall design: There are 4 normal uterine tract and 5 infectious uterine tract samples. Differential gene expression between each group (Infectious vs. Normal) are compared.

研究目的：本研究旨在对感染性牛子宫内膜组织开展RNA测序（RNA-seq）分析，以揭示子宫感染后调控子宫生理状态的关键基因与生物学通路。
研究方法：采用Illumina测序平台完成RNA测序。使用FastQC对FASTQ格式的单端测序读段进行质量评估，从读段的3'端与5'端修剪低质量碱基，直至获得Phred质量值为30（对应准确率99.9%）及以上的碱基；同时过滤掉平均质量评分低于30、序列长度小于30个核苷酸的无效读段。使用HiSAT2将清理后的有效读段比对至牛参考基因组（Bos_taurus.ARS-UCD1.2）。将生成的SAM格式文件进行排序，并通过SAMtools工具转换为BAM格式文件。借助HTSeq工具包中的htseq-count脚本，生成比对至牛基因模型的读段计数数据。使用Bioconductor的DESeq2包，分析感染组与正常子宫组织组之间的差异表达基因。
研究结论：本研究证实，牛子宫内膜肉阜间区域发生子宫感染后，会出现多个与炎症反应、免疫应答、子宫生理、子宫微环境及生育能力相关的基因与通路表达异常。
实验设计：本研究共纳入4例正常子宫组织样本与5例感染性子宫组织样本，对两组（感染组vs.正常组）的差异基因表达水平进行比较分析。