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Reproductive system metagenome

ABSTRACT: the microbiota in uterine flush samples at 30 DPP Raw sequence reads

PROVIDER: PRJNA380397 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5371543_1.fastq.gz	Fastqsanger.gz
	SRR5371543_2.fastq.gz	Fastqsanger.gz

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Project description:All cows experience bacterial contamination and tissue injury in the uterus postpartum, instigating a local inflammatory immune response. However mechanisms that control inflammation and achieve a physiologically functioning endometrium, while avoiding disease in the postpartum cow are not succinctly defined. This study aimed to identify novel candidate genes indicative of inflammation resolution during involution in healthy beef cows. Previous histological analysis of endometrial inflammation showed a great degree of inflammation 15 days postpartum (DPP) which significantly decreased by 30 DPP. The current study generated a genome-wide transcriptomic profile of endometrial biopsies at both time points using mRNA-Seq. The pathway analysis tool GoSeq identified KEGG pathways enriched by significantly differentially expressed genes elevated at both time points. Novel candidate genes of inflammatory resolution were subsequently validated in additional postpartum animals using quantitative real-time PCR (qRT-PCR). Endometrial biopsies were collected as part of a previous study 15 and 30 days postpartum (DPP) from 13 mixed breed beef multiparous cows. The endometrial transcriptomic profiles from endometrial biopsies were assessed by mRNA-Seq (n=3) and candidate gene expression was measured by qRT-PCR (n=5) comparing 15 DPP to 30 DPP samples. Reads were mapped to the bovine genome with TopHat, Htseq-count summarized the number of aligned reads per exon and EdgeR normalized the data and returned significantly differentially expressed genes. GoSeq identified KEGG pathways enriched by significantly differentially expressed genes elevated at both time points.

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Uterine infection-induced transcriptomic changes in the bovine endometrium

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.

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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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