RNA-seq data of endometrium from Yorkshire pigs
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA593965 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10598550_1.fastq.gz | Fastqsanger.gz | |||
| SRR10598550_2.fastq.gz | Fastqsanger.gz | |||
| SRR10598551_1.fastq.gz | Fastqsanger.gz | |||
| SRR10598551_2.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq data of endometrium from Yorkshire pigs
2020-06-16 | GSE141564 | GEO
Project description:BACKGROUND: Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large percentage of the developing conceptuses are lost. However, the gene expression and regulatory networks in the endometrium contributing to the establishment of the maternal: placental interface remain poorly understood. RESULTS: We characterized the endometrial gene expression profile during the peri-implantation stage of development by comparing two breeds that demonstrate very different reproductive efficiencies. We employed the porcine Affymetrix GeneChip® to assay the transcriptomic profiles of genes expressed in the uterine endometrium obtained from Meishan and Yorkshire gilts (n = 4 for each breed) on day 12 of gestation (M12 and Y12, respectively). Total of 17,076 probesets were identified as "present" in at least two arrays. A mixed model-based statistical analysis predicted a total of 2,656 (q < 0.1) transcripts as differentially expressed between Meishan and Yorkshire pigs. Eighteen differentially expressed transcripts of interest were validated by quantitative real-time PCR. Gene ontology (GO) annotation revealed that the known functions of the differentially expressed genes were involved in a series of important biological processes relevant to early pregnancy establishment in the pig. CONCLUSIONS: The results identified endometrial gene expression profiles of two breeds differing in litter size and identified candidate genes that are related to known physiological pathways related to reproductive prolificacy. These findings provide a deeper understanding of molecular pathways differing between two breeds at the critical peri-implantation stage of pregnancy, which can be utilized to better understand the events contributing to pregnancy establishment in the pig. Meishan and Yorkshire breeds endometirum were selected and RNA been extracted and hybridized to the Affymetrix microarray. A number of genes have been shown differently expressed on two breeds.
2014-05-21 | E-GEOD-46332 | biostudies-arrayexpress
Project description:BACKGROUND: Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large percentage of the developing conceptuses are lost. However, the gene expression and regulatory networks in the endometrium contributing to the establishment of the maternal: placental interface remain poorly understood. RESULTS: We characterized the endometrial gene expression profile during the peri-implantation stage of development by comparing two breeds that demonstrate very different reproductive efficiencies. We employed the porcine Affymetrix GeneChip® to assay the transcriptomic profiles of genes expressed in the uterine endometrium obtained from Meishan and Yorkshire gilts (n = 4 for each breed) on day 12 of gestation (M12 and Y12, respectively). Total of 17,076 probesets were identified as "present" in at least two arrays. A mixed model-based statistical analysis predicted a total of 2,656 (q < 0.1) transcripts as differentially expressed between Meishan and Yorkshire pigs. Eighteen differentially expressed transcripts of interest were validated by quantitative real-time PCR. Gene ontology (GO) annotation revealed that the known functions of the differentially expressed genes were involved in a series of important biological processes relevant to early pregnancy establishment in the pig. CONCLUSIONS: The results identified endometrial gene expression profiles of two breeds differing in litter size and identified candidate genes that are related to known physiological pathways related to reproductive prolificacy. These findings provide a deeper understanding of molecular pathways differing between two breeds at the critical peri-implantation stage of pregnancy, which can be utilized to better understand the events contributing to pregnancy establishment in the pig.
2014-05-21 | GSE46332 | GEO
Project description:Affymetrix miRNA arrays were used to generate miRNA profiles of on the endometrium of Meishan and Yorkshire pigs on days 15 (implantation stage), 26 (post-implantation stage) and 50 (mid-gestation stage) of gestation. The study allowed for the determination of the miRNAs that were differentially expressed in porcine endometrium on different gestational day and breed. The majority of the miRNAs were differentially expressed during the implantation stage. This study will provide the information to better understanding of the role miRNAs in the porcine endometrium during pregnancy.
2014-11-19 | GSE35995 | GEO
Project description:Intramuscular fat (IMF) content is an important trait closely correlated with meat quality, which is highly variable among swine breeds from diverse genetic backgrounds. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA-sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. A total of 717 differentially expressed genes (DEGs) were identified in our study, with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. GO analysis showed that DEGs significantly related to muscle proliferation and development, lipid storage and catabolic, extracellular matrix structural constituent, and neutral amino acid transmembrane transporter activity. Pathway analysis revealed that DEGs associated with fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, protein digestion and absorption, and amino acid metabolism. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs from both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes for affecting pork quality.
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Project description:sRNA Sequencing during Skeletal Muscle Development between Tongcheng Pigs and Yorkshire Pigs
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Project description:The study allowed for the determination of the mRNAs that were differentially expressed in porcine endometrium on different gestational day and breed. The majority of the mRNAs were differentially expressed during the implantation stage. This study will provide the information to better understanding of the role of these differently expressed mRNAs in the porcine endometrium during pregnancy. Affymetrix mRNA arrays were used to generate mRNA profiles of on the endometrium of Meishan and Yorkshire pigs on days 15 (implantation stage), 26 (post-implantation stage) and 50 (mid-gestation stage) of gestation.
2015-12-31 | GSE51787 | GEO
Project description:Affymetrix miRNA arrays were used to generate miRNA profiles of on the endometrium of Meishan and Yorkshire pigs on days 15 (implantation stage), 26 (post-implantation stage) and 50 (mid-gestation stage) of gestation. The study allowed for the determination of the miRNAs that were differentially expressed in porcine endometrium on different gestational day and breed. The majority of the miRNAs were differentially expressed during the implantation stage. This study will provide the information to better understanding of the role miRNAs in the porcine endometrium during pregnancy. the endometrium form different gestational day and breed were collected. In order to determine the miRNA expression profile of these tissue, RNA was extracted, labeled and hybridized on an Affymetrix miRNA array.
2014-11-19 | E-GEOD-35995 | biostudies-arrayexpress
Project description:We investigated the heart tissue whole-genome DNA methylation data of Tibetan and Yorkshire pigs raised at high and low altitudes using MeDIP-seq (methylated DNA immunoprecipitation sequencing) technologies, in order to comparatively analyze epigenetic regulation in the two breeds under normoxic and hypoxic conditions. In addition, we aimed to identify the key genes and molecular mechanisms that are involved in adaptation to high altitude in the Tibetan pig. The results of bisulphite sequencing and RT-qPCR indicated that the differentially methylated genes identified in MeDIP-seq were credible. Our results provide new insights into the molecular mechanisms and the epigenetic mechanism involved in hypoxic adaptation in pigs, and a greater understanding of human hypoxic diseases.
2018-05-23 | GSE114779 | GEO
Project description:The study allowed for the determination of the mRNAs that were differentially expressed in porcine endometrium on different gestational day and breed. The majority of the mRNAs were differentially expressed during the implantation stage. This study will provide the information to better understanding of the role of these differently expressed mRNAs in the porcine endometrium during pregnancy. Affymetrix mRNA arrays were used to generate mRNA profiles of on the endometrium of Meishan and Yorkshire pigs on days 15 (implantation stage), 26 (post-implantation stage) and 50 (mid-gestation stage) of gestation. The endometrium from different gestational day and breed were collected. In order to determine the mRNA expression profile of these tissue, RNA was extracted, labeled and hybridized on an Affymetrix mRNA array.
2015-12-31 | E-GEOD-51787 | biostudies-arrayexpress