Genome-wide differential expression profiling of ovarian circRNAs associated with litter size in pigs
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PROVIDER: PRJNA562823 | ENA |
REPOSITORIES: ENA
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Project description:In this study, porcine ovaries with smaller or larger litter size (SLS or LLS) were subjected to high-throughput RNA-sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig. Besides, 411 miRNAs were identified, and of these 17 were significantly down-regulated and 16 miRNAs were up-regulated when comparing sows with LLS and SLS, respectively. In addition, we identified a total of 3,556 lncRNA candidates, of which 96 lncRNAs were up-regulated and 206 lncRNAs were down-regulated when comparing LLS to SLS. 16,428 genes were detected, and 2,392 unigenes were significantly differently expressed at the LLS and SLS ovarian samples. In addition, a competitive endogenous RNA (ceRNA) network was constructed. Our study indicates that non-coding RNAs may play roles in modulating porcine litter size.
2019-09-05 | GSE136592 | GEO
Project description:Circular RNAs (circRNAs) have been emerging as an important regulator in mammalian reproduction via acting as miRNA sponges. However, the circRNAs in porcine ovaries related with litter size remains largely unknown. In this study, porcine ovaries with smaller or larger litter size (LLS) were subjected to high-throughput RNA sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig (|log2 (fold change) | > 1, FDR < 0.05). Bioinformatics predicted that most of circRNAs harbored miRNA binding sites, and the expression patterns of circRNAs and their putative binding miRNAs were validated by qPCR. Moreover, the expression of circ-TCP11/miR-183 was significantly reversely correlated and their direct interaction was confirmed by dual-luciferase assay. Our study indicates that circRNAs may play potential effects on modulating porcine litter size.
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Project description:This study provide an opportunity to elucidate the genetic control of fetal implantation and improve our understanding of fetal implantation and gestation maintenance, thus make further improvement for litter size of pigs.
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Project description:This study provide an opportunity to elucidate the genetic control of fetal implantation and improve our understanding of fetal implantation and gestation maintenance, thus make further improvement for litter size of pigs. Nine pregnant sows were slaughtered by electrical on day 13, day 18 and day 24 after insemination (the pregnant group, three sows every period). The non-pregnant sows were slaughtered on day 13 after inseminated (n=3).In pregnant sows, samples of the endometrium attachment sites and inter-sites were taken. Samples from the endometrium of the non-pregnant sows were taken from comparable locations.
2015-01-26 | E-GEOD-51970 | biostudies-arrayexpress
Project description:Analysis of gene expression in the lungs of pigs from high and low litter birth weight groups (HBW and LBW) inoculated with swine influenza virus. The aim of the experiment is to determine whether litter birth weight has an effect on the innate immune response to infection in pigs, and whether differences in gene expression can be linked to epigenetic differences between the two birth weight groups.
2015-10-27 | GSE62765 | GEO
Project description:Fatty pigs are characterized by a thrifty genotype, adapted to harsh environments based on changes in metabolism and energy saving. Thus, we hypothesized that feto-maternal energy partitioning in large litters might have postnatal effects that might be independent of intrauterine growth restriction (IUGR) processes. Hence, the current work reported the influence of two effects on postnatal performance and carcass and meat quality of purebred Iberian pigs: (a) the effects of the number of piglets in the litter (high vs. low litter size), and (b) the effects of birthweight (low (LBW) vs. normal (NBW)) in large litters. The results confirmed that NBW piglets born in large litters had differences in developmental patterns of weight, back-fat deposition, and fatty acid (FA) composition when compared to NBW piglets from small litters. These results were different from those found in LBW piglets when compared to their NBW counterparts, which showed an initial asymmetrical growth and altered muscle FA composition at slaughtering. The assessment of FA composition indicated better metabolic status in NBW piglets from large litters than in LBW piglets. These data support the concept that the prenatal environment, even when the individual may cope with it, inescapably affects postnatal life.
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Project description:Embryonic survival rate is an important factor for the fecundity of sows, and it is affected by endometrium secreting histotroph. A higher concentration of calcium ion has been observed in the uterus of the high prolific Erhualian sows (EH) compared with low prolific ones (EL), which suggests EH sows had a greater establishment and maintenance of pregnancy, and thus increase embryonic survival rate during peri-implantation period. In order to understand the mechanisms of endometrium secreting histotroph affecting embryonic survival rate during Erhualian peri-implantation period, the expression patterns of endometrial mRNA in the EH and EL on day 12 of gestation were analyzed using RNA sequencing technology. 164 differentially expressed genes (DEGs) were identified (Padj < 0.05, |log2(FC)| ≥ 1)，including 46 upregulated and 118 downregulated genes in the EH group compared with EL group. Among these DEGs, 17 DEGs have been previously reported as DEGs in other pig breeds for litter size. Gene Ontology (GO) enrichment indicated that a subset of DEGs were involved in the calcium ion binding and cell adhesion. Solute carrier family 8 member A3 (SLC8A3) and solute carrier family 24 member 4 (SLC24A4) were upregulated genes (Padj < 0.05) in EH group and they were considered as key candidate genes expressed in endometrium to affect embryonic survival rate during peri-implantation period. The present results will aid in understanding the variation of litter size in Erhualian breed during peri-implantation period.
2019-05-31 | GSE122983 | GEO
Project description:Analysis of gene expression in the lungs of pigs from high and low litter birth weight groups (HBW and LBW) inoculated with swine influenza virus. The aim of the experiment is to determine whether litter birth weight has an effect on the innate immune response to infection in pigs, and whether differences in gene expression can be linked to epigenetic differences between the two birth weight groups. A two condition experiment: lung tissue RNA from HBW and LBW SIV-infected pigs. 16 biological replicates for each condition, each hybridized with a reference to separate arrays. 32 arrays in total.
2015-10-27 | E-GEOD-62765 | biostudies-arrayexpress
Project description:Comparison of gene expression in the lungs of pigs classified as Resistant (RES) or Susceptible (SUS) to influenza pathology based on clinical lesion scores. The aim of the experiment is to identify genes whose expression is associated with resistance/susceptibility to influenza pathology. These are a subset of animals selected from a larger experiment that investigated the effect of low (LBW) or high (HBW) litter birth weight phenotype on influenza pathology.
2015-10-27 | GSE62768 | GEO
Project description:To explore the overall circRNAs involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (cotyledons emergence, rosette leavesï¹¥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and sequenced by the Illumina HiSeq2500 platform. We obtained 31 Gb raw data and identified 1217 circRNAs with expression quantity. We annotated these circRNAs and predicted their targeted microRNA. The circRNAs involved in growth and development of Arabidopsis thaliana across lifespan were identified and analyzed using the Illumina HiSeq2500 platform.
2016-09-01 | E-GEOD-77672 | biostudies-arrayexpress