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Bovine reproductive tract sample

ABSTRACT: Bovine reproductive tract sample Raw sequence reads

PROVIDER: PRJNA1129596 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR29649200_1.fastq.gz	Fastqsanger.gz
	SRR29649200_2.fastq.gz	Fastqsanger.gz
	SRR29649201_1.fastq.gz	Fastqsanger.gz
	SRR29649201_2.fastq.gz	Fastqsanger.gz
	SRR29649202_1.fastq.gz	Fastqsanger.gz

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Bovine reproductive tract sample

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TRANSCRIPTOMIC ANALYSIS OF BOVINE ENDOMETRIUM WITH SHORT UTERINE TRACT LEADING TO INFERTILITY

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.

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Project description:In internally fertilizing species, the first direct molecular contact between the male and female gene products occurs within the female reproductive tract – a highly complex and rapidly evolving structure in many species. While molecular interactions between sperm and oocyte have received a lot of attention, efforts to gain insight into the crosstalk happening during the sperm cells journey to the site of fertilization have been limited, especially in mammals. The interactions between sperm cells and the female reproductive tract not only facilitate sperm guiding, storage, and protection against introduced pathogens but also comprise a sophisticated mechanism of female-mediated sperm selection. Molecular interaction partners that are involved directly in sperm assessment and selection, however, are difficult to pinpoint within the massive immunological response happening in the female reproductive tract following copulation. While we have some knowledge of sperm surface proteins interacting with the components of the female reproductive tract, the female counterparts of these interactions are still largely unknown. We characterized the murine female transcriptional response to semen following copulation. We mated males and females from different strains and used strain-specific SNPs to distinguish semen-derived from female reproductive tract-derived transcripts. We specifically focused on the different subdivisions of the female reproductive tract, with the aim to identify female molecules directly involved in sperm assessment. Our results show a large number of differentially expressed genes in uterus, uterotubal junction and oviduct compared to unmated control and significant differences in differential expression between the subsections.

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