Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of pabpn1l ko and wt female mice oocytes and zygotes

ABSTRACT: After the library was qualified, the library was pooled according to the effective concentration and the demand of target offline data, and was sequenced by Illumina platform. Since PABPN1L can bind the poly(A) tail, we propose that it participates in the process of post-transcriptional regulation and degradation of maternal mRNA. We investigated the mRNA changes in GV oocytes, MII oocytes, and fertilized eggs using RNA-seq. GV oocytes, MII oocytes and zygotes were collected and mixed from three mice of each genotypes separately.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Mus musculus

SUBMITTER: Mingxi Liu

PROVIDER: E-MTAB-9488 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of oocytes and zygotes from pabpn1l ko and wt female mice

Project description:PABPN1L participates in the process of post-transcriptional regulation and degradation of maternal mRNA.We collect samples of each period from pabpn1l ko and wt female mice during different stages. Each group contained a total of 30 oocytes or zygotes. In the initial step, we spiked 2 × 106 mRNA-EGFP, transcribed in vitro, into each group.Then, RNA was extracted and detected.Reverse transcription was performed on the samples that met the effective concentration.After quality inspection, build the library.GV oocytes, MII oocytes and zygotes were collected from three different PABPN1L KO or WT mice seperately.

2021-03-26 | E-MTAB-10233 | biostudies-arrayexpress

RNA-seq from oocytes and zygotes of pabpn1l ko and wt female mice during different stages

Project description:PABPN1L participates in the process of post-transcriptional regulation and degradation of maternal mRNA.So,we collect samples of each period from pabpn1l ko and wt female mice during different stages.Then, RNA was extracted and detected.Reverse transcription was performed on the samples that met the effective concentration.After quality inspection, build the library.GV oocytes, MII oocytes and zygotes were collected from three different PABPN1L KO or WT mice separately.

2021-03-19 | E-MTAB-10199 | biostudies-arrayexpress

Transcriptome assay of materal mRNA degradation in Btg4-deleted oocytes

Project description:We analyzed the functions of BTG family proteins in maternal mRNA degradation in mouse oocytes. By comparing the degradation of transcripts in WT oocytes and KO oocytes, we are able to know the defects in maternal mRNA clearance in BTG4-deleted oocytes, and identified the BTG4 target genes in oocyte cyplasmic maturation. 2 WT oocyte samples at GV stage, 2 WT oocyte samples at MII stage, 2 Btg4-/- oocyte samples at GV stage and 2 Btg4-/- oocyte samples at MII stage?2 WT embryo samples at zygote stage, 2 WT embryo samples at 2-cell stage, 2 Btg4-/- embryo samples at zygote stage and 2 Btg4-/- embryo samples at 2-cell stage , and a WT GV oocyte, a WT MII oocyte, a Erk-/- GV oocyte and a Erk-/- MII oocyte are performed RNA sequencing.

2016-03-16 | E-GEOD-71257 | biostudies-arrayexpress

Quantitative proteomic analysis of both fresh and vitrified porcine GV oocytes during in vitro maturation

Project description:In this study, we used tandem mass tag (TMT)-based quantitative approach to acquire proteomic profiles of porcine GV and MII oocytes and MII oocytes vitrified at the GV stage.

2021-07-01 | PXD023107 | Pride

Transcriptome analysis of mouse Cnot6l-/- preovulatory oocytes (GV), ovulated eggs (MII), and 1-cell zygotes

Project description:We profiled transcriptomes from Cnot6l deadenylase knock-out mouse GV oocytes, MII eggs and 1-cell zygotes in order to analyse its function during the oocyte-to-embryo (OET) transition. Transcriptome of wild-type golden hamster GV oocytes was also profiled.

2018-07-10 | GSE116771 | GEO

TMT-based proteomics analysis of GV, GVBD and MII oocytes

Project description:Two replicates of GV, GVBD, and MII oocytes were subjected to the 6-plex TMT labeling, HP-RP fractionation, and LC-MS/MS analysis. Two labeling experiments were performed for the total four replicates of each stage of oocytes.

2022-02-15 | PXD018777 | Pride

Microarray profiling of YTHDF2 deficient mouse oocytes

Project description:To study the role of the protein YTHDF2 during female gametogenesis, its gene was conditionally deleted in oocytes. Total RNA samples from YTHDF2 deficient GV and MII oocytes (and control oocytes) were subjected to array profiling.

2018-02-12 | E-MTAB-5576 | biostudies-arrayexpress

Characterization and parental contribution of piRNAs and endo-siRNAs to mouse zygotes.

Project description:Transposable elements (TEs) are widely represented in eukaryotic genomes. Recently, a set of small RNAs known as rasRNAs (repeat-associated small RNAs) have been related to the down-regulation of TEs conferring a means to safeguard genome integrity. Two key members of the rasRNAs group are piRNAs and endo-siRNAs. In this study, we have performed a comparative analysis of piRNAs and endo-siRNAs present in mouse oocytes, spermatozoa and zygotes, identified by deep sequencing and bioinformatic analysis. Both piRNAs and endo-siRNAs regulate TEs in addition to other repetitive elements such as tRNAs and rRNAs, suggesting an alternative role of rasRNAs with regard to translation regulation. The detection of piRNAs and endo-siRNAs in sperm cells and revealed also in zygotes, hints to their potential delivery to oocytes during fertilization. However, a comparative assessment of the three cell types indicates that both piRNAs and endo-siRNAs are mainly maternally inherited. Finally, we have assessed the role of the different rasRNA molecules in connection with amplification processes by way of the M-bM-^@M-^\ping-pong cycleM-bM-^@M-^]. Our results suggest that the ping-pong cycle can act on other rasRNAs, such as tRNA- and rRNA-derived fragments, thus not only being restricted to TEs during gametogenesis, as was evidenced in spermatozoa, oocytes and zygotes. Comparative analysis from deep sequencing of piRNAs and endo-siRNAs in mouse oocytes, spermatozoa and zygotes

2014-05-20 | E-GEOD-45983 | biostudies-arrayexpress

Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition

Project description:Maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the maternal environment of oocyte transits to the zygotic genome driven expression program, and terminally differentiated oocyte and sperm are reprogrammed to totipotency. Metaphase II (MII) oocytes and zygotes (one-cell embryo) serve as the mature oocyte and the initiation of pre-implantation embryo development respectively, and characterizing their molecular landscapes at protein levels plays an important role in uncovering MZT and zygotic genome activation (ZGA )in mammals. Here we used an ultrasensitive proteomic approach to depict an in-depth landscape for the very early stage of mouse MZT.

2023-05-23 | PXD041399 | Pride

Transcription profiling of immature germinal vesicle stage oocytes with mature metaphase II oocytes to identify and characterize the changed and stable transcripts during mouse oocyte maturation.

Project description:There is massive destruction of transcripts during maturation of mouse oocytes. The objective of this project was to identify and characterize the transcripts that are degraded versus those that are stable during the transcriptionally silent germinal vesicle (GV)-stage to metaphase II (MII)-stage transition using the microarray approach. A system for oocyte transcript amplification using both internal and 3'-poly(A) priming was utilized to minimize the impact of complex variations in transcript polyadenylation prevalent during this transition. Transcripts were identified and quantified using Affymetrix Mouse Genome 430 v2.0 GeneChip. The significantly changed and stable transcripts were analyzed using Ingenuity Pathways Analysis and GenMAPP/MAPPFinder to characterize the biological themes underlying global changes in oocyte transcripts during maturation. It was concluded that the destruction of transcripts during the GV to MII transition is a selective rather than promiscuous process in mouse oocytes. In general, transcripts involved in processes that are associated with meiotic arrest at the GV-stage and the progression of oocyte maturation, such as oxidative phosphorylation, energy production, and protein synthesis and metabolism, were dramatically degraded. In contrast, transcripts encoding participants in signaling pathways essential for maintaining the unique characteristics of the MII-arrested oocyte, such as those involved in protein kinase pathways, were the most prominent among those stables. Experiment Overall Design: Comparison immature GV-stage oocyte (3 biological replicates) with mature MII-stage oocytes (3 biological replicates)

2007-11-13 | E-GEOD-5668 | biostudies-arrayexpress

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