RNA-seq of female gonads isolated from juvenile eif4e1b mutant and wild-type zebrafish
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1008624 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25744342_1.fastq.gz | Fastqsanger.gz | |||
| SRR25744342_2.fastq.gz | Fastqsanger.gz | |||
| SRR25744343_1.fastq.gz | Fastqsanger.gz | |||
| SRR25744343_2.fastq.gz | Fastqsanger.gz | |||
| SRR25744344_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:The mRNA cap-binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish, we isolated gonads with a high expression of ziwi:GFP (female germline marker) from wild-type and eif4e1b mutant juveniles and performed RNA-seq.
2023-10-03 | GSE241537 | GEO
Project description:We have identified eukaryotic translation initiation factor 4E family member 1B (Eif4e1b) as a regulator of maternal RNA translation, whose maternal deletion leads to 2-cell arrest phenotype in mouse embryos. eIF4E1b protein binds mRNA selectively in oocytes and controls their translation in early embryos. We aim to profile the global changes in protein expression in metaphase II (MII) eggs and zygotes collected from control or Eif4e1b knockout female mice. An encapsulated proteomic-sample processing protocol is used to perform this low-input mass spectrometry to quantify proteomic changes (Kulak et al. 2014/PMID 24497582).
2023-06-12 | PXD041583 | Pride
Project description:Single cell transcriptomic analyses are increasingly being employed to study human developmental processes in the gonad to advance our understanding of human gametogenesis. However, to date, these analyses have primarily focused on germ cells, while the somatic niche has been largely overlooked. Moreover, a comparative transcriptomic analysis of both female and male early gonad development on the single cell level is currently lacking. We performed single cell RNA-Seq on whole human fetal gonads from first and second trimester, both from male and female. We define gene expression profiles, which include novel marker genes, of major gonadal somatic cell types and validate them on the protein level. We identify the genetic signature of early human male rete cells, both in male and in female gonads. Overall, our study provides an in-depth molecular characterization of both male and female somatic cell types in early fetal gonads.
2024-01-02 | GSE181558 | GEO
Project description:Maternal mRNAs are essential for protein synthesis during oogenesis and early embryogenesis. To adapt translation to specific needs during development, maternal mRNAs are translationally repressed by shortening the polyA tails. While mRNA deadenylation is associated with decapping and degradation in somatic cells, maternal mRNAs with short polyA tails are stable. Here we report an essential role for the germline-specific paralog of the mRNA cap-binding factor eIF4E, known as eIF4E1b, in the storage and repression of maternal mRNAs with short polyA tails. eIF4E1b binds to the mRNA cap and is targeted to ribonucleoprotein complexes through its direct interaction with eIF4ENIF1/4E-T. In early embryos, eIF4E1b binds to a specific set of translationally repressed mRNAs with short or no polyA tails, such as histone mRNAs, which are translated later on during embryogenesis. Consistent with an important role in maternal mRNA dormancy, mutation of eIF4E1b in zebrafish impairs female germline development. Understanding the mechanism and function of eIF4E1B provides new insights into fundamental post-transcriptional regulatory principles governing early vertebrate development.
2024-04-12 | PXD042434 | Pride
Project description:To identify mRNAs loaded onto eIF4E1B and eIF4E, LACE-seq was performed using eIF4E1B and eIF4E immunoprecipitated mRNAs from mouse fully grown oocytes RNA co-precipitated with eIF4E1B and eIF4E differed from the control RNA enriched by the control IgG rabbit serum antibody.
2023-02-21 | GSE213866 | GEO
Project description:MicroRNAs (miRNAs) are a highly conserved class of small RNAs which function in a sequence-specific manner to post-transcriptionally regulate expression of target genes. Tissue-specific miRNA expression studies have discovered numerous functions for miRNAs in various aspects of embryonic development, but a role for miRNAs in gonadal development and sex differentiation has not yet been reported. Using the chicken embryo as a vertebrate model, differential miRNA expression between male and female embryonic gonads, was analysed at three developmental stages (embryonic days (E) 5.5, E6.5 and E9.5), using custom-designed 4x2K CombiMatrix miRNA microarray. The aims of this study were to: 1-identify miRNAs differentialy expressed by sex; 2-identify sex-specific miRNAs; 3-analyse global changes in miRNA up-regulation in male versus female gonads before, during and after the histological onset of sexual differentiation. This study provides a basis for establishing whetehr miRNAs are involved in either initiating or regulating vertebrate gonadal sex differentiation. Keywords: miRNA, sex comparison, developmental stage comparison. miRNA samples from male and female embryonic chicken gonads from three developmental stages: embryonic day (E) 5.5 (Hamilton & Hamburger (HH) stage 27-28), E6.5 (HH stage 29-30) & E9.5 (HH stage 35-36). Samples are listed with biological replicates used for analysis in brackets following: 1 - Male E5.5 (5); 2 - Female E5.5 (4); 3 - Male E6.5 (5); 4 - Female E6.5 (3); 5 - Male E9.5 (4); 6 - Female E9.5 (4).
2010-05-18 | E-GEOD-13154 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a highly conserved class of small RNAs which function in a sequence-specific manner to post-transcriptionally regulate expression of target genes. Tissue-specific miRNA expression studies have discovered numerous functions for miRNAs in various aspects of embryonic development, but a role for miRNAs in gonadal development and sex differentiation has not yet been reported. Using the chicken embryo as a vertebrate model, differential miRNA expression between male and female embryonic gonads, was analysed at three developmental stages (embryonic days (E) 5.5, E6.5 and E9.5), using custom-designed 4x2K CombiMatrix miRNA microarray. The aims of this study were to: 1-identify miRNAs differentialy expressed by sex; 2-identify sex-specific miRNAs; 3-analyse global changes in miRNA up-regulation in male versus female gonads before, during and after the histological onset of sexual differentiation. This study provides a basis for establishing whetehr miRNAs are involved in either initiating or regulating vertebrate gonadal sex differentiation. Keywords: miRNA, sex comparison, developmental stage comparison.
2008-10-11 | GSE13154 | GEO
Project description:Transcriptional profiling of the mantle tissue across the four stages of female gonads development (winter peak) in a natural population of the marine mussel Mytilus galloprovincialis sampled in the Bizerta Lagoon, Tunisia, across November 2007 -March 2008. Background: Seasonal environmental changes may affect the physiology of Mytilus galloprovincialis (Lam.), an intertidal filter-feeder bivalve occurring commonly in Mediterranean and Atlantic coastal areas. We investigated seasonal variations in relative transcript abundance of the digestive gland and the mantle (gonads) of males and females. To identify gene expression trends, we used a medium-density cDNA microarray (1.7 K probes) in dual-color competitive hybridization analyses. Results: Hierarchical clustering of digestive gland microarray data showed two main branches, distinguishing profiles associated with the “hot” months (May–August) from the other months. Genes involved in chitin metabolism, associated with mussel nutrition and digestion, showed higher expression during summer. Moreover, we found different gene expression patterns in the digestive glands of males and females during the four stages of mussel gonadal development. Microarray data from gonadal transcripts also displayed clear patterns during the different developmental phases with peak relative mRNA abundance at the ripe phase (stage III) for both sexes. Conclusion: These data showed a clear temporal pattern in gene expression profiles of mussels sampled over an annual cycle. Physiological response to thermal variation, food availability, and reproductive status across months may contribute to variation in gene expression.
2011-06-06 | GSE23049 | GEO
Project description:We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cell proliferation, and carcinogenesis. Unexpectedly, we detected a novel sRNA type, the tRFs, which are 30–36-nt RNA fragments derived from tRNA molecules, in gonads
2014-07-27 | GSE57414 | GEO
Project description:We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cell proliferation, and carcinogenesis. Unexpectedly, we detected a novel sRNA type, the tRFs, which are 30–36-nt RNA fragments derived from tRNA molecules, in gonads Determination miRNA, piRNA and tRF expression in swine gonads
2014-07-27 | E-GEOD-57414 | biostudies-arrayexpress