RNA-seq analysis of swine reproductive tissues including endometrium, oviduct and ovary through the estrous
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA427706 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6425080_1.fastq.gz | Fastqsanger.gz | |||
| SRR6425080_2.fastq.gz | Fastqsanger.gz | |||
| SRR6425090_1.fastq.gz | Fastqsanger.gz | |||
| SRR6425090_2.fastq.gz | Fastqsanger.gz | |||
| SRR6425100_1.fastq.gz | Fastqsanger.gz |
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Project description:The underlying genomic regulation of the tissue synchronization is poorly understood. To understand this better we investigated the transcriptomes of the porcine ovary, endometrium, and oviduct at days 0, 3, 6, 9, 12, 15, or 18 of the oestrous cycle. We analysed the transcriptome profiles of the individual tissues.
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Project description:The endometrium provides optimal conditions for the transport of sperm to the oviduct, to the site of fertilization, and later on for the reception of the embryo. To study these changes on the level of gene expression, a messenger RNA expression profiling of endometrium tissue samples collected from 19 cyclic heifers at five stages of the estrous cycle (days 0, 3.5, 12, 18, 20) was performed. RNA was extracted from these tissue samples and analyzed with a custom-made bovine oviduct and endometrium (BOE) cDNA array. The cDNAs present on the array were derived from several previously conducted differential gene expression studies of bovine endometrium between different stages of the estrous cycle, during early pregnancy, and from studies of bovine oviduct epithelial cells. In all of these studies cDNAs of differentially expressed genes were identified using a combination of subtracted cDNA libraries and cDNA array hybridization. 1,440 cDNA fragments are located on the array. Twenty radioactively labeled cDNA samples (n=4 for each cycle stage) were hybridized with BOE arrays. Raw data were normalized using the BioConductor package vsn. Keywords: time course of gene expression in bovine endometrium during estrous cycle Nineteen German Fleckvieh (Simmental) heifers were slaughtered at four different days of the estrous cycle, four animals at day 0, four at day 3.5, three at day 12 and eight animals at day 18. Four of the day 18 animals showed high and the other four low serum progesterone (P4) levels, respectively. This resulted in five groups of endometrial tissue samples corresponding to five stages of the estrous cycle.
2010-05-27 | E-GEOD-8337 | biostudies-arrayexpress
Project description:The endometrium provides optimal conditions for the transport of sperm to the oviduct, to the site of fertilization, and later on for the reception of the embryo. To study these changes on the level of gene expression, a messenger RNA expression profiling of endometrium tissue samples collected from 19 cyclic heifers at five stages of the estrous cycle (days 0, 3.5, 12, 18, 20) was performed. RNA was extracted from these tissue samples and analyzed with a custom-made bovine oviduct and endometrium (BOE) cDNA array. The cDNAs present on the array were derived from several previously conducted differential gene expression studies of bovine endometrium between different stages of the estrous cycle, during early pregnancy, and from studies of bovine oviduct epithelial cells. In all of these studies cDNAs of differentially expressed genes were identified using a combination of subtracted cDNA libraries and cDNA array hybridization. 1,440 cDNA fragments are located on the array. Twenty radioactively labeled cDNA samples (n=4 for each cycle stage) were hybridized with BOE arrays. Raw data were normalized using the BioConductor package vsn. Keywords: time course of gene expression in bovine endometrium during estrous cycle
2007-12-31 | GSE8337 | GEO
Project description:Female fertility in mammals requires the iterative remodeling of the entire adult female reproductive tract across the menstrual/estrous cycle. Here we examine global transcriptional dynamics of the mouse oviduct along the anteroposterior axis and across the estrous cycle. Though we observed robust patterns of differential oviduct gene expression along the anteroposterior axis, we found surprisingly few changes in gene expression across the estrous cycle, in marked contrast to other mammals. We speculate that this is an evolutionarily derived state that may reflect the extremely rapid five-day mouse estrous cycle.
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Project description:Here we tested the hypothesis that intrauterine infusion of pathogenic bacteria leads to changes in the transcriptome of the reproductive tract in dairy cattle three months later. We used virgin Holstein heifers to avoid the confounding effects of periparturient problems, metabolic stress and lactation. Animals were infused intrauterine with endometrial pathogenic bacteria Escherichia coli and Trueperella pyogenes to induce clinical endometritis (n = 4) and compared with control animals (n = 6). Three months after infusion, the caruncular and intercaruncular endometrium, isthmus and ampulla of the oviduct, and granulosa cells from dominant ovarian follicles were profiled by RNA-sequencing. Compared with control, bacterial infusion altered the transcriptome of all the tissues. Most differentially expressed genes were tissue-specific, with 109 differentially expressed genes unique to the caruncular endometrium, 57 in the intercaruncular endometrium, 65 in the isthmus, 298 in the ampulla, and 83 in granulosa cells. Surprisingly, despite infusing the bacteria into the uterus, the granulosa cells had more predicted upstream regulators of differentially expressed genes than all the other tissues combined. In conclusion, there was evidence of long-term changes to the transcriptome of the endometrium, oviduct and even the granulosa cells after intrauterine infusion of pathogenic bacteria, which implies that all these tissues contribute to the infertility that persists after endometritis.
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Project description:The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from 5 time points of the estrous cycle (D0, D3, D8, D12, and D16) was performed to study the dynamics of endometrial gene expression. Endometrial biopsies were collected from five mares (Bavarian Warmblood) at the respective time points. Samples were divided and subjected to isolation of RNA for microarray analysis and analysis of tissue composition. Blood samples were collected to determine serum progesterone levels for every sample. Statistical analysis of microarray data revealed almost 10,000 differential probes corresponding to 4,996 differentially expressed genes. A cluster analysis based on gene expression profiles during the estrous cycle revealed 8 major gene expression profiles: mRNAs with highest levels 1) at D0, 2) from D0 to D3, 3) at D3, 4) from D3 to D8, 5) at D8, 6) from D8 to D12, 7) from D12 to D16, and 8) at D16. DAVID Functional Annotation Clustering revealed overrepresentation of distinct functional terms in different phases of the cycle, e.g. ‘extracellular matrix’ and ‘protein transport’ during estrus, ‘DNA replication and ‘cell cycle’ during early luteal phase, ‘endoplasmic reticulum’ and ‘protein transport’ in the luteal phase, and ‘inflammatory response’ in the late luteal and follicular phase. Expression of selected genes of the expression clusters was validated by quantitative Real-time PCR (qPCR). This study provides new insights into global changes of equine endometrial gene expression during the estrous cycle.
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Project description:This study attempted to reveal the profile of the oviductal gene expression at each stage of estrous cycle by microarray analyses
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