Translatome of aged mouse NEBD – stage oocytes determined using a new polysomal profiling method
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA637383 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11927722_1.fastq.gz | Fastqsanger.gz | |||
| SRR11927722_2.fastq.gz | Fastqsanger.gz | |||
| SRR11927723_1.fastq.gz | Fastqsanger.gz | |||
| SRR11927723_2.fastq.gz | Fastqsanger.gz | |||
| SRR11927724_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:We provide complete translatome of mouse oocytes from aged females after the breakdown of nuclear envelope (NEBD). RNAseq of polysomal and non-polysomal RNA was determined by using a novel approach combining polysomal fractionation of 200 NEBD-staged oocytes in small SW55Ti centrifugation tubes in the absence of any external spike and qRT-PCR analysis of ribosomal RNA in collected fractions. We compared these data to the translatome of same stage oocytes from young females (GSE121358). We report that genome-wide translatome profiling reveals considerable numbers of transcripts that are differentially translated in oocytes obtained from aged compared to young females. Additionally, we show the majority of aberrantly translated mRNAs in older oocytes have roles associated with cell cycle regulation. Indeed, we demonstrate the differential translation rates of four specific maternal age related transcripts (Sgk1, Castor1, Aire and Eg5) are associated with distinct localization patterns around the newly forming meiotic spindle.
2021-01-01 | GSE151836 | GEO
Project description:Transcriptional activation in mammalian embryos occurs in a stepwise manner. In mice, it begins at the late one-cell stage, followed by a minor wave of activation at the early two-cell stage, and then the major genome activation (MGA) at the late two-cell stage. Cellular homeostasis, metabolism, cell cycle, and developmental events are orchestrated before MGA by time-dependent changes in the array of maternal transcripts being translated (i.e., the translatome). Despite the importance of maternal mRNA and its correct recruitment for development, neither the array of recruited mRNA nor the regulatory mechanisms operating have been well cheracterized. We present the first comprehensive analysis of changes in the maternal component of the zygotic translatome during the transition from oocyte to late one-cell stage embryo, revealing global transitions in the functional classes of translated maternal mRNAs, and apparent changes in the underlying cis-regulatory mechanisms. Batches of 160-500 MII oocytes or one-cell embryos. 4 independent replicates per sample kind. Lysed and processed for polysomal mRNA extraction. Two rounds of IVT.
2007-12-07 | E-GEOD-3962 | biostudies-arrayexpress
Project description:Translatomes are more accurate than transcriptomes as indicators of gene expression profiles in cells, especially in cellular processes that cease transcriptional expression and rely on translational control, such as oocytes. Here, we developed a dual omics methodology to simultaneously examine gene expression using the transcriptomes and translatomes of single oocytes or embryos and identified a protein that can promote human oocyte maturation. First, we developed a transcriptome and translatome sequencing (T&T seq) strategy using single mouse oocytes and extended this method to human oocytes and early embryos. Many genes that are differentially expressed through translational control at different developmental stages and between two species were identified using this method. Overall, our dual omics methodology opens a new avenue for simultaneously assessing the transcriptome and translatome of a cell. We developed a dual omics methodology to simultaneously examine gene expression using the transcriptomes and translatomes of single oocytes or embryos and identified a protein that can promote human oocyte maturation. First, we developed a transcriptome and translatome sequencing (T&T seq) strategy using single mouse oocytes.
2022-07-25 | GSE197578 | GEO
Project description:We subjected MCF7 cells to starvation with 0.5% charcoal treated serum for 48h and then we added 17-beta estradiol (E2) at final concentration of 10 nM, profiling before and after 60 minutes of treatment the transcriptome and the translatome, coming from the polysomal pool of mRNAs after sucrose gradient separation. Comparison of translatome profile changes with corresponding transcriptome profile changes represents a way of studying translational control networks and the degree of concordance between cellular controls affecting mRNA abundance and cellular controls affecting mRNA availability to translation. It is well known that E2 is a strong transcriptional regulator, while its translational control activity is less characterized. To provide a direct experimental evaluation of E2 induced translational regulation, we compared translatome and transcriptome profiles of E2 treated cells. Keywords: polysomal profiling, translatome profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, estradiol stimulation, estrogen receptor. The comparison between transcriptional and polysomal profiling was used for the discovery of general and mRNA-specific changes in the translation state of the serum starved MCF7 cells transcriptome in response to E2 stimulus. To identify translationally regulated mRNA molecules, gene expression signals derived from the polysomal populations were compared by microarrays analysis to those obtained from unfractionated total RNAs. Polysomal RNA and total RNA were isolated from MCF7 cells serum starved and treated with E2. Cells lysates were collected before (t = 0 min) and after (t = 60 min) E2 treatment. All experiments were run in quadruplicates.
2010-12-31 | E-GEOD-22012 | biostudies-arrayexpress
Project description:Transcriptome and translatome analyses of mouse and human oocytes
| PRJNA811110 | ENA
Project description:au14-10_wd40 - effet of light on translatome of arabidopsis seeds during germination - Does light regulates germination via polysome association ? - At harvest seeds are dormant.They stay dormant if stored at -20°C.A.Th dormant seeds dont germinate at 25°C in darkness.Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients)were extracted from imbibed seeds for 20h at 22°C in darkness and light(3 biological replicates). Transcriptome and translatome are compared for light vs dark for 20h of imbibition. In silico comparison will allow to compare transcriptome and translatome for each type of sample.
2017-02-01 | GSE93181 | GEO
Project description:We subjected MCF7 cells to starvation with 0.5% charcoal treated serum for 48h and then we added 17-beta estradiol (E2) at final concentration of 10 nM, profiling before and after 60 minutes of treatment the transcriptome and the translatome, coming from the polysomal pool of mRNAs after sucrose gradient separation. Comparison of translatome profile changes with corresponding transcriptome profile changes represents a way of studying translational control networks and the degree of concordance between cellular controls affecting mRNA abundance and cellular controls affecting mRNA availability to translation. It is well known that E2 is a strong transcriptional regulator, while its translational control activity is less characterized. To provide a direct experimental evaluation of E2 induced translational regulation, we compared translatome and transcriptome profiles of E2 treated cells. Keywords: polysomal profiling, translatome profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, estradiol stimulation, estrogen receptor.
2010-12-31 | GSE22012 | GEO
Project description:Several genome-wide transcriptome analyses that focused on p53-induced cellular responses in many cellular contexts have continued to expand the already vast p53-regulated transcriptional networks. To investigate post-transcriptional controls as an additional dimension of p53-directed gene expression responses we performed translatome analysis by polysomal profiling on MCF7 cells treated with Doxorubicin and Nutlin-3a. A comparison between the transcriptome and the translatome revealed a large number of uncoupled genes, whose transcription changes did not correlate with translation changes. Overall, we establish p53 as a master regulator of translational control and identify many p53 target genes affecting translation that can contribute to p53-dependent cellular responses. Keywords: p53, transcriptome, translatome, polysomal RNA, subpolysomal RNA, uncoupling, Doxorubicin, Nutlin-3a Total RNA (tot) was extracted from MCF7 vector cells after 16h of treatment with Doxorubicin (1.5uM) and Nutlin-3a (10uM) or DMSO (solvent, as control treatment). Polysomal profiling was performed after the same conditions. We collected all subpolysomal mRNA fractions (sub) and the polysomal ones (pol) after sucrose gradient fractionation of cytoplasmic lysates to analyze separately mRNAs that are not actively translated from those that are considered in active translation, respectively. Experiments were performed in three biological replicates.
2014-04-17 | E-GEOD-50650 | biostudies-arrayexpress
Project description:Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. This study uncovers the reshaping undergoing in the translational control system of the host in response to staphylococcal α-hemolysin oligomers (rAHL). Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF. The comparison between translatome and transcriptome profiling was used to discover mRNA-specific changes of the SH-SY5Y cells transcriptome and translatome in response to staphylococcal α-hemolysin oligomers (rAHL). To identify translationally regulated mRNAs, gene expression signals derived from the polysomal mRNA populations were compared by microarrays analysis to those obtained from total RNAs. Polysomal mRNA and total mRNA were isolated from SH-SY5Y cells treated with 3nM of extracted oligomers (rAHL) for 2 hours. Cells lysates were collected from untreated cells (control) and from treated cells. All experiments were run in biological triplicates.
2015-04-01 | E-GEOD-60543 | biostudies-arrayexpress
Project description:Translatome analysis by sucrose gradient centrifugation of cell lysates followed by microarray profiling of the polysomal and subpolysomal RNA fractions represents a way of both studying translational control networks and better approximating the proteomic representation of cells. It is an established notion that translational control takes place essentially at the translation initiation level, therefore the variation in abundance of a given mRNA species on polysomes can be directly related to the variation in abundance of the corresponding protein. Comparison of translatome profile changes with corresponding transcriptome profile changes can provide a measure of the degree of concordance between cellular controls affecting mRNA abundance and cellular controls affecting mRNA availability to translation. To provide a direct experimental evaluation of the phenomenon, we decided to study a classical example of transcriptional reprogramming of gene expression: Epidermal Growth Factor (EGF) treatment. This stimulus triggers a well known chain of intracellular transduction events, ultimately resulting in a multifaceted phenotypic spectrum of changes with prevalent induction of cell growth and proliferation. We subjected HeLa cells to serum starvation for 12h and then we added EGF at final concentration of 1 μg/ml, profiling before and after 40 minutes of treatment the transcriptome, the translatome, coming from the polysomal pool of mRNAs after sucrose gradient separation, and also the mRNA content of the subpolysomal pool, expected not to be actively translated. Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, EGF starvation release. The comparison between transcriptional and polysomal profiling was used for the discovery of general and mRNA-specific changes in the translation state of the serum starved HeLa cells transcriptome in response to EGF stimulus. To identify translationally regulated mRNA molecules, gene expression signals derived from the polysomal and subpolysomal RNA populations were compared by microarrays analysis to those obtained from unfractionated total RNAs. Polysomal RNA, subpolysomal RNA and total RNA were isolated from HeLa cells serum starved and treated with EGF. Cells lysates were collected before (t = 0 min) and after (t = 40 min) EGF treatment. All experiments were run in triplicates.
2010-05-27 | E-GEOD-20277 | biostudies-arrayexpress