Ontology highlight
ABSTRACT:
PROVIDER: PRJNA795608 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17499000_1.fastq.gz | Fastqsanger.gz | |||
| SRR17499000_2.fastq.gz | Fastqsanger.gz | |||
| SRR17499001_1.fastq.gz | Fastqsanger.gz | |||
| SRR17499001_2.fastq.gz | Fastqsanger.gz | |||
| SRR17499002_1.fastq.gz | Fastqsanger.gz |
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Project description:Ovarian follicle selection plays an important role in the reproduction of sexually mature hens, and this process can directly affect the growth and development of follicles until the final ovulation, thus affecting laying performance and fecundity of hens. In the laying hen ovary, one follicle from a cohort of 8-13 follicles of 6-8 mm in diameter is selected daily to enter the preovulatory hierarchy. In this study, we globally compared the proteomes of chicken ovarian follicles before and after follicle selection. A total of 5883 proteins were identified in the proteomes of chicken 6-8 mm prehierarchical follicles and 12-15 mm hierarchical follicles. 259 proteins are differentially expressed in 12-15 mm hierarchical follicle compared with prehierarchical follicle, of which 175 proteins are up-regulated and 84 proteins are down-regulated. The Gene Ontology enrichment of differentially expressed proteins revealed enriched GO terms for peptidase activity, acrosin binding for their molecular function and in the process of negative regulation of peptidase activity, and regulation of fertilization. The KEGG pathway analysis indicated that differentially expressed proteins were enriched for ribosome, lysine degradation, and endocytosis pathways. Nine differentially expressed proteins including vitellogenin-1 were validated with Parallel Reaction Monitoring (PRM) analysis, and their functions were discussed. This study provided a global proteomic view of the development of chicken ovarian follicles, which will serve as a foundation for understanding the molecular signatures and pathways of follicle selection in hens.
2021-09-08 | PXD011470 | Pride
Project description:we compared the phosphoproteomes of SY and F6 follicles in laying hens and identified several genes involved in chicken follicle selection.
2022-09-01 | PXD029503 | Pride
Project description:The differences in reproductive processes at the molecular level between viviparous and oviparous animals are evident, and the site in the ovary that synthesizes sex hormones (androgens and oestrogens) and the trends for enriching sex hormones during follicle development in chickens are different from those in mammals, suggesting that the effect of sex hormones on follicle development in chickens is probably different from that in viviparous animals. To explore the specific role of androgen receptors (ARs) on chicken follicular development, we matched the correspondence of follicular development stages among chickens, humans, cows and identified chicken-specific genes related to follicle development (GAL-SPGs) by comparing follicle development-related genes and their biological functions among species (chickens, humans, and cows). A comparison of the core transcription factor regulatory network of granulosa cells (or ovaries) based on super enhancers among species (chicken, human, and mouse) revealed that AR is a core transcriptional regulator specific to chickens. In vivo experiments showed that inhibition of AR significantly reduced the number of syf (selected stage follicles) in chickens and decreased the expression of GAL-SPGs in F5 follicles, while in vitro experiments showed that inhibition of AR expression in chicken granulosa cells (GCs) significantly down-regulated the expression levels of GAL-SPGs, indicating that AR could regulate follicle selection through chicken-specific genes related to follicle development. A comparison among species (77 vertebrates) of the conserved genomic regions, where chicken super-enhancers are located, revealed that the chicken AR super-enhancer region is conserved in birds, suggesting that the role of AR in follicle selection may be widespread in birds. In summary, we found that AR can regulate follicle selection through chicken-specific genes related to follicle development, which also emphasizes the important role of AR in follicle selection in chickens and provides a new perspective for understanding the unique process of follicle development in chickens.
2021-08-16 | GSE182083 | GEO
Project description:The aim of study was to identify the differentially expressed genes in SYF by using Illumina RNA deep sequencing, one SYF has the highest expression level of FSHR, the other has the lowest expression level of FSHR. We sampled six follicles from three chickens.In order to discover the key genes that regulate the process of follicle selection. From RNA-seq results, we got 26.63G reads,when mapping the reads to chicken genome, 75.13%-78.40% reads were successfully mapped, and more than 98% reads were unique.and we found 1382 new genes,functional annotation of the new gene was also performed.
2017-12-06 | GSE100673 | GEO
Project description:Follicles of polycystic ovaries (PCO) often become arrested in early antral stages at around 3 to 11 mm in diameter. The condition disturbs dominant follicle selection and may result in altered ovulation and anovulation. During the growth and development of human follicles, the follicular fluid (FF) constitutes the avascular microenvironment in which the oocyte develops and acts as a vehicle for hormone signaling between cues from circulation and follicular cells. Previous proteomics studies performed on FF from women with polycystic ovarian syndrome (PCOS) have revealed information on the protein changes associated with the pathophysiology of this disorder. However, these studies have been conducted on FF samples obtained in connection with oocyte pick-up during ovarian stimulation right at the time of ovulation and are limited to follicular conditions during the follicular phase of the menstrual cycle. This study aimed to detect proteomic alterations in FF from human small antral follicles (hSAF) obtained from women with PCO as compared to normal women.
2022-04-07 | PXD031485 | Pride
Project description:Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by hair follicle stem cells (HFSCs). We used RNA-seq to identify SOX9-dependent transcriptional changes and ChIP-seq to identify SOX9-bound genes in HF-SCs. Telogen quiescent hair follicle stem cells (HFSCs) and intefollicular epidermal cells (IFE) were FACS-purified for ChIP-sequcencing and HFSCs for RNA-Sequencing
2014-01-28 | E-GEOD-54424 | biostudies-arrayexpress
Project description:Primordial follicles are the first class of follicles formed in the mammalian ovary and are comprised of an oocyte surrounded by a layer of squamous pre-granulosa cells. This developmental class remains in a non-growing state until individual follicles activate to initiate folliculogenesis. What regulates the timing of follicle activation and the upstream signals that govern these processes are major unanswered questions in ovarian biology. This is partly due to the paucity of data on staged follicle cells since isolating and manipulating individual oocytes and somatic cells from early follicle stages are challenging. To date, most studies on isolated primordial follicles have been conducted on cells collected from animal-age- or oocyte size-specific samples, which encompass multiple follicular stages. Here, we report a method for collecting primordial follicles and their associated oocytes and somatic cells from neonatal murine ovaries using liberase, DNase I, and Accutase. This methodology allows for the identification and collection of follicles immediately post-activation enabling unprecedented interrogation of the primordial-to-primary follicle transition. Molecular profiling by single-cell RNA sequencing (scRNA-seq) revealed that processes including organelle disassembly and cadherin binding were enriched in oocytes and somatic cells as they transitioned from primordial to the primary follicle stage. Furthermore, targets including WNT4, TGFβ, FOXO3, and a network of transcription factors were identified in the transitioning oocytes and somatic cells as potential upstream regulators that collectively may drive follicle activation. Taken together, we have developed a more precise characterization and selection method for studying staged-follicle cells, revealing several novel regulators of early folliculogenesis.
2022-06-29 | GSE206681 | GEO
Project description:Thecal tissue forms a layer around the follicle just prior to antral stage and grows with the follicle (containing an oocyte) as it matures. The innermost component (theca interna) supplies hormones and other factors necessary to the growth and development of the granulosa and oocyte. Most follicles regress and die (become atretic) at the antral stage, and this process as well as development of the follicle are undoubtedly influenced by the theca. Transcriptional changes in ovarian theca interna at the global level were examined by microarray during atresia and development to improve our understanding of the mechanisms involved. Four groups of bovine ovarian follicles were selected for analysis . Follicle size, type and array number for each group are, small (3-5 mm) healthy rounded (n=5), healthy columnar (n=5), atretic(n=5) and large healthy (>9mm), (n=4). For each group, the RNA from the theca interna of a single follicle was used to hybridise an array.
2014-05-20 | E-GEOD-49505 | biostudies-arrayexpress
Project description:Intense selective breeding of broiler breeds of chickens has resulted in suboptimal egg production in broiler breeder hens. Ad libitum feeding which leads to excessive and disorganized follicular growth exacerbates this reproductive phenotype. One strategy used to improve broiler breeder hen reproductive efficiency is restricted feeding. In this study, we sought to identify transcriptional changes which translate level of dietary intake to increased follicle selection. Broiler breeder hens were raised according to commercial guidelines until 28 weeks of age and then randomly assigned to an ad libitum diet (FF) or continued on a restricted diet (RF) for 6 weeks. Following dietary treatment, granulosa cells from growing 6-8 mm follicles from FF hens (n=3) and RF hens (n=3) were collected, RNA was extracted, and samples were processed for RNA-sequencing on Illumina NextSeq 500. Transcriptomes of granulosa cells from 6-8 mm follicles were sequenced to identify transcriptional differences in the population from which follicles are selected into the preovulatory stage. FastQ files were first processed through trim-galore and reads were aligned to the Galgal6 genome using the RNA-seq aligner, STAR. A cluster analysis using hclust in R identified a FF sample as an outlier and this sample was removed from the analysis. Differential expression analysis was conducted using DeSEQ2 and resulted in 350 differentially expressed genes. Several genes involved in follicle selection were upregulated in prehierarchal follicles of FF hens, suggesting an effect of dietary treatment at early stages in follicle development.
2021-09-23 | GSE175887 | GEO