Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome and translatome analyses of mouse and human oocytes

ABSTRACT: Transcriptome and translatome analyses of mouse and human oocytes

PROVIDER: PRJNA811110 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18175300_1.fastq.gz	Fastqsanger.gz
	SRR18175300_2.fastq.gz	Fastqsanger.gz
	SRR18175301_1.fastq.gz	Fastqsanger.gz
	SRR18175301_2.fastq.gz	Fastqsanger.gz
	SRR18175302_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 228

Similar Datasets

Transcriptome and translatome analyses of mouse and human oocytes

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

Translatome of aged mouse NEBD – stage oocytes determined using a new polysomal profiling method

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

Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation

Project description:Translational regulation plays a critical role during oocyte-to-embryo transition including zygotic genome activation. However, the translatome during OET and molecular mechanisms underlying human ZGA remain largely uncharted. Here, we integrated ultra-low-input Ribo-seq with RNA-seq (R2-lite) to jointly profile the translatome and transcriptome from the same samples across 8 stages in human oocytes and early embryos. These data not only unveil conservation and divergence of the translation landscapes between human and mouse OET, but also identify critical regulators of human ZGA.

2022-10-08 | GSE197265 | GEO

Translatome of aged mouse NEBD – stage oocytes determined using a new polysomal profiling method

Project description:Translatome of aged mouse NEBD – stage oocytes determined using a new polysomal profiling method

| PRJNA637383 | ENA

Translatome analyses of HEK293T upon NSP12 overexpression

Project description:Translatome analyses of HEK293T upon NSP12 overexpression

| PRJNA757696 | ENA

Simultaneous deep transcriptome and proteome profiling in single mouse oocytes

Project description:Deep proteome data in the single-cell multi-omics analysis of single mouse oocytes.

2023-07-20 | PXD043935 |

Identifying the translatome of mouse NEBD – stage oocytes via SSP-profiling; a novel polysome fractionation method

Project description:Meiotic maturation of oocyte relies on pre-synthesized maternal mRNA, the translation of which is highly coordinated in space and time. Here, we provide a detailed polysome profiling protocol utilising small SW55Ti ultracentrifugation tubes with a volume of 5 ml. This newly optimized method, named Scarce Sample Polysome Profiling (SSP-profiling), is suitable for both scarce and conventional sample sizes and is compatible with downstream RNA-seq to identify polysome associated transcripts. Utilising SSP-profiling we have assayed the translatome of mouse oocytes at the onset of nuclear envelope breakdown (NEBD); a developmental stage that has thus far remained unexplored. Our analyses have identified 1778 transcripts with moderate to strong polysome occupancy, including abundantly represented mRNAs encoding mitochondrial and ribosomal proteins, proteoasomal components, glycolytic and amino acids synthetic enzymes, proteins involved in cytoskeleton organization plus RNA-binding and translation initiation factors. In addition to transcripts encoding known players of meiotic progression, we have also identified several mRNAs encoding proteins of unknown function. Polysome profiles generated using SSP-profiling were more than comparable to those developed using existing conventional approaches, being demonstrably superior in their resolution, reproducibility, versatility, speed of derivation and downstream protocol applicability.

2020-02-12 | GSE121358 | GEO

Identifying the Translatome of WT and Lsm14b KO GV-Stage Oocytes in mice via Scarce Sample Polysome Profiling (SSP-profiling)

Project description:RNA-binding proteins (RBPs) have essential functions during oocyte development.In order to explore the regulatory role of RNA-binding protein LSM14B in oocyte, we Identified the translatome of WT and Lsm14b KO GV-Stage Oocytes in mice via Scarce Sample Polysome Profiling (SSP-profiling).

2023-09-08 | GSE206270 | GEO

Identifying the translatome of mouse NEBD – stage oocytes via SSP-profiling a novel polysome fractionation method

Project description:Identifying the translatome of mouse NEBD – stage oocytes via SSP-profiling a novel polysome fractionation method

| PRJNA497118 | ENA

Distinct transcriptome, translatome, and proteome reprogramming during the oocyte-to-embryo transition

Project description:The oocyte-to-embryo transition converts terminally differentiated gametes into a totipotent embryo. Fertilized embryos undergo the resetting of the transcriptional program as the zygotic genome is activated from a silenced state started from the late-stage oocyte. How transcriptome, translatome, and proteome interplay in this critical developmental window remains poorly understood. Utilizing a highly sensitive mass spectrometry, we obtained high-quality proteome landscapes including nearly 6,000 genes spanning 10 stages, from the mouse full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. By integrative analysis with corresponding transcriptomes and translatomes, we found transcription and translation levels can not reflect protein abundance in most cases. From FGOs to the 4-cell embryos, the proteomes are predominated by FGO-produced proteins, while the transcriptome and the translatome are much more dynamic. FGO-originated proteins frequently persist in embryos after the corresponding transcripts are already downregulated or decayed. Improved concordance between protein and RNA is observed for genes starting translation only upon meiotic resumption or transcribed only in embryos, although the detected protein dynamics often lag behind transcription and translation. Concordance between protein and transcription/translation is associated with protein half-lives. Finally, a kinetic model well predicts protein dynamics when incorporating both the initial protein abundance in FGO and translation kinetics across developmental stages. In sum, our study reveals multilayer control of gene expression during oocyte maturation and embryogenesis.

2023-06-27 | PXD035696 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data