Filtered reproductive long non-coding RNAs by genome-wide analyses of goat ovary at different estrus periods
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ABSTRACT:
PROVIDER: PRJNA494579 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7961910.fastq.gz | Fastqsanger.gz | |||
| SRR7961910_1.fastq.gz | Fastqsanger.gz | |||
| SRR7961910_2.fastq.gz | Fastqsanger.gz | |||
| SRR7961911.fastq.gz | Fastqsanger.gz | |||
| SRR7961911_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: The goat is an important farm animal. Reproduction is an important process of goat farming. The ovary is the most important reproductive organ for goats. In recent years, an increasing number of long non-coding RNAs (lncRNAs) have been implicated in the regulation of mammal reproduction. However, there are few studies on the function of lncRNAs in reproduction, particularly lncRNAs in the ovary. Results: The sequencing of goat ovaries generated 1,122,014,112 clean reads, and 4,926 lncRNAs and 1,454 TUCPs(transcripts of uncertain coding potential) were identified for further analysis by using the coding potential analysis software, CNCI, CPC and Pfam-sca. There were 115 /22 differential lncRNAs /TUCPs transcripts between the ovaries of the luteal phase and the follicular phase. We predicted the target genes of lncRNA /TUCP based on co-expression and co-localization methods. In total, 2584 /904 target genes were predicted by co-expression, and 326/73 target genes were predicted by co-localization. The functions of these target genes were further analyzed with GO and KEGG analysis. The results showed that lncRNAs /TUCPs, which are highly expressed in goat ovaries in the luteal phase, are mainly associated with the synthesis of progesterone, and we filtered the lncRNAs /TUCPs, such as XR_001918177.1 and TUCP_001362, which may regulate the synthesis of progesterone; lncRNAs /TUCPs, which are highly expressed in goat ovaries in the follicular phase, are mainly associated with oogenesis and the maturation of oocytes, and we filtered the lncRNAs /TUCPs that may regulate the oogenesis and maturation of oocyte, such as XR_001917388.1 and TUCP_000849. Conclusion: The present study provided the genome expression profile of lncRNAs /TUCPs in goat ovaries at different estrus periods and filtered the lncRNAs /TUCPs associated with goat reproduction. These results are helpful to further study the molecular mechanisms of goat reproduction.
2018-11-15 | GSE120144 | GEO
Project description:BACKGROUND:The goat is an important farm animal. Reproduction is an important process of goat farming. The ovary is the most important reproductive organ for goats. In recent years, an increasing number of long non-coding RNAs (lncRNAs) have been implicated in the regulation of mammal reproduction. However, there are few studies on the function of lncRNAs in reproduction, particularly lncRNAs in the ovary. RESULTS:The sequencing of goat ovaries generated 1,122,014,112 clean reads, and 4926 lncRNAs and 1454 TUCPs (transcripts of uncertain coding potential) were identified for further analysis by using the coding potential analysis software, CNCI, CPC and Pfam-sca. There were 115 /22 differential lncRNAs /TUCPs transcripts between the ovaries of the luteal phase and the follicular phase. We predicted the related genes of lncRNA /TUCP based on co-expression and co-localization methods. In total, 2584 /904 genes were predicted by co-expression, and 326/73 genes were predicted by co-localization. The functions of these genes were further analyzed with GO and KEGG analysis. The results showed that lncRNAs /TUCPs, which are highly expressed in goat ovaries in the luteal phase, are mainly associated with the synthesis of progesterone, and we filtered the lncRNAs /TUCPs, such as XR_001918177.1 and TUCP_001362, which may regulate the synthesis of progesterone; lncRNAs /TUCPs, which are highly expressed in goat ovaries in the follicular phase, are mainly associated with oogenesis and the maturation of oocytes, and we filtered the lncRNAs /TUCPs that may regulate the oogenesis and maturation of oocyte, such as XR_001917388.1 and TUCP_000849. CONCLUSION:The present study provided the genome expression profile of lncRNAs /TUCPs in goat ovaries at different estrus periods and filtered the potential lncRNAs /TUCPs associated with goat reproduction. These results are helpful to further study the molecular mechanisms of goat reproduction.
| S-EPMC6278114 | biostudies-literature
Project description:The yak estrus is a seasonal phenomenon, probably involving the epigenetic regulation of the synthesis and secretion of sex hormones as well as the growth and development of follicles. In this study, we collected the yak ovarian tissues at the three different states of anestrus, estrus, and pregnancy, and obtained the full transcriptome m6A map in yak by MeRIP-seq. The RT-qPCR showed that the expression of METTL3, METTL14, FTO, YTHDC1 were significantly different across different periods in the ovaries. Next, we identified 20174, 19747 and 13523 m6A peaks in the three ovarian samples of YO-A, YO-F and YO-P using the methylated RNA immunoprecipitation sequencing (MeRIP-seq). The m6A peaks are highly enriched in the coding sequence (CDS) region and 3′untranslated region (3′UTR) as well as the conserved sequence of “RRACH.” Functional analysis revealed the involvement of m6A in many physiological activities of the yak’s ovary during estrus and pregnancy. The association analysis found that some genes such as BNC1, HOMER1, BMP15, BMP6, GPX3, and WNT11 were related to ovarian functions. The comparison of the distribution patterns of methylation peaks in the ovarian tissues across different periods further explored the m6A markers related to the regulation of ovarian ovulation and follicular development in the yak ovary. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the yak ovary.
2021-07-22 | GSE180401 | GEO
Project description:Background:The morphology of vaginal secretions during estrus and diestrus is characteristic and easy to distinguish. There are also significant differences in hormone levels between the two periods in physiological condition. However, the gene changes during estrus cycle especially the two periods are still unclear. Therefore, this study plans to find out the pathway changes related to the estrus cycle of female mice, the expression of various proteins, predict the genes sensitive to hormone changes in vivo through gene analysis of 15 tissues in the two periods and construct of differential gene expression library. Methods:The wildtype healthy female mice in estrus were compared with those in diestrus. The transcriptome changes between the two periods were probed by using high-throughput RNA-seq techniques. Results:A comprehensive mouse transcriptome map in estrus or diestrus across fifteen tissues including aorta, vein, brown adipose tissue, white adipose tissue, heart, kidney, liver, skeletal muscle, stomach, duodenum, cerebrum, hypothalamus, ovary, womb and spleen were provided. Conclusions:This dataset could serve as a baseline resource for investigating the potential gene changes sensitive to the estrus cycle across different tissues and provide the information for screening the key functional genes or molecular markers of estrus cycle.
2022-12-17 | GSE131172 | GEO
Project description:The aim of the study was to assess the cellular composition and transcriptional changes at single-cell resolution of the female reproductive tract across the four stages of estrus cycle in young adult mice (ovary, oviduct, uterus, cervix and vagina, with spleen as a comparison) and compared this with similar analyses of decidualization (uterus) and ageing (ovary, oviduct, uterus, cervix, vagina and spleen). Vaginal smears were used to stage the estrus cycle in young mice. To collect the decidualized uteri mice were mated and uterine tissue was collected from pregnant mice at day 5.5 after mating. Tissues of aged mice were collected at the age of 18 months. All tissues were collected and digested using a collagenase and trypsin protocol to obtain single cell suspension. Libraries were prepared using the 10x scRNA-seq protocol.
2023-02-01 | E-MTAB-11491 | biostudies-arrayexpress
Project description:Background: Small ungulates (sheep and goat) display a seasonal breeding, characterised by successive periods of sexual activity (SA) and sexual rest (SR). In sexual activity period the ovarian cycle of females is active and ready for reproduction (oestrus) whereas in sexual rest no ovulation and reproduction are possible (deep anoestrus). Odours emitted by a sexually active male can reactivate the ovarian cycle of anoestrus females. The plasticity of the olfactory system under these hormonal changes has never been explored at the peripheral level of odours reception. As it was shown in pig that the olfactory secretome (proteins secreted in the nasal mucus) could be modified under hormonal control, we monitored its composition in females of both species along several seasons, thanks to a non-invasive sampling of olfactory mucus. Results: In both species the olfactory secretome is composed of isoforms of OBP-like proteins, generated by post-translational modifications, phosphorylation, N-glycosylation and O-GlcNAcylation. Important changes were observed in the olfactory secretome between the sexual rest and the sexual activity periods, characterised in ewe by the specific expression of SAL-like proteins and the emergence of OBPs O-GlcNAcylation. In Goat, the differences between SA and SR did not come from new proteins expression, but from different post-translational modifications, the main difference between the SA and SR secretome being the number of isoforms of each protein. Conclusion: Despite common behaviour, seasonal breeding, and genetic resources, the two species seem to adapt their sensory equipment in SA by different modalities: the variation of olfactory secretome in ewe could correspond to a specialization to detect male odours only in SA, whereas in goat the stability of the olfactory secretome could indicate a constant capacity of odours detection suggesting that the hallmark of SA in goat could be the emission of specific odours by the sexually active male.
2019-11-06 | PXD014833 | Pride
Project description:Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia. Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps.
2021-06-05 | GSE176157 | GEO
Project description:In comparison with cow milk, goat (Capra hircus) milk contains much higher levels of unsaturated fatty acids, as well as higher levels of total fat, proteins, carbohydrates, calcium, and vitamins.The main objective of the present study was to better define the relationship of known miRNAs regulating milk fat metabolism. Our main purpose is to search for some known miRNAs regulating milk fat metabolism, to this end, we screened potential miRNAs with differential expression between peak-lactation and non-lactation.
2016-06-25 | GSE83706 | GEO
Project description:Milk fatty acids secreted by the mammary glands are one of the most important determinants of the nutritional value of goat milk. However, there are few data available on the transcriptome-wide changes across lactation in the goat. In this study, goat mammary tissue from the periods encompassing lactation, cessation of milking and involution were used for digital gene expression sequencing (DGE) using the goat transcriptome as reference sequence. A total of 51299 unigenes were identified and annotated to 12763 genes, of which 9131 genes were differentially expressed (DEG) among the various stages of lactation. Functional classification through KOG, GO, and KEGG was used for selection of the top expressed genes and the differentially expressed genes (DEG). DEG series-cluster analysis revealed 16 possible expression patterns. Using co-expression analysis, within the lipid transport and metabolism KOG categories, PLA2, CPT1, PLD had the most number of correlated genes. GGA, SRPRB and AP4S1 were the top 3 with the highest number of correlated genes associated with intracellular trafficking, secretion, and vesicular transport. These data may provide candidate genes with a high probability of having functional roles in regulating of goat fatty acid metabolism during the various stages of lactation.
2017-09-01 | GSE87089 | GEO