GSE209699
TRANSCRIPTOMIC ANALYSIS OF BOVINE ENDOMETRIUM WITH SHORT UTERINE TRACT LEADING TO INFERTILITY
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. Overall design: There are 4 normal uterine tract and 5 short uterine tract samples. Differential gene expression between each group (Short vs. Normal) are compared.