Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation profiles of mouse sperm in response to antibiotic-induced gut microbiota dysbiosis using whole-genome bisulfite sequencing

ABSTRACT: DNA methylation profile of mouse sperm from conventionally-raised mice and gut dysbiosis experienced mice were characterized using whole-genome bisulfite sequencing. Genome-wide DNA methylation changes between control and dysbiotic male�s sperm were highly comparable, with no change in DNAme globally or at genomic features, only 21 differentially methylated regions (DMR) were identified, which did not overlap known regulatory elements. Epididymal sperm samples were harvested from 11 weeks old inbred male mice that were experiencing gut microbiota dysbiosis for 6-week (antibiotics treated, n=5), or drink sterilized water (control, n=5).

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-10033 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome profiles of paternal testis and their offspring in response to gut microbiota dysbiosis using RNA sequencing analysis

Project description:Tissue samples harvested from conventionally-raised sire and their offspring or dysbiotic sire and their offspring were profiled for transcriptome changes using total RNA sequencing. Total RNA was extracted from four different tissue types: sire testis, F1 placenta (at E13.5 & E18.5), and F1 brain and brown adipose tissue (at postnatal day P17).Testis were harvested from 11-weeks inbred male mice that were experiencing gut microbiota dysbiosis for 6-week (antibiotics treated, n=5), or drink sterilized water (control, n=5). While, F1 offspring samples were collected from three independent matings per group and two offspring samples per litter.

2023-11-13 | E-MTAB-10034 | biostudies-arrayexpress

Genomic profiling of offspring liver tissue in response to paternal gut microbiota dysbiosis using whole genome sequencing

Project description:Liver tissue samples were harvested from offspring sired by conventionally-raised male mice or dysbiotic sire, and profiled for genome changes using whole genome sequencing. F1 offspring samples were collected from six independent mating, and gDNA was extracted from offspring liver at postnatal day P17.

2023-11-13 | E-MTAB-10273 | biostudies-arrayexpress

Proteome analyses of sperm from wild type, Akap3 and Akap4 gene null mutant mice

Project description:PKA signaling plays important functions during mouse spermatogenesis and for the regulation of sperm motility. The efficiency of PKA signaling is regulated partly by its binding protein A-kinase anchoring protein (AKAP) family. Mature mouse sperm contain several AKAPs, of which AKAP3 and AKAP4 are localized in the principal piece of sperm tail and they are sperm-specific. Using gene knock-out mouse models, it was found that both AKAP3 and AKAP4 are essential for the formation of a complete fibrous sheath, the electron-dense sub-cellular structure within sperm flagellum that is important for the motility of sperm and male fertility. Lack of AKAP3 or AKAP4 caused aberrant sperm morphology and inmotility, leading to eventual male sterility. In the present study, we investigated the changes of cellular proteome in the absence of AKAP3 or AKAP4 in mature sperm, using quantitative mass spectrometry. It was found that global changes of sperm proteome occur in the absence of AKAP3 or AKAP4. In Akap3 null sperm, proteins related to flagella structure, PKA signaling and motility regulations are down-regulated, whereas proteins involved in RNA metabolism, protein translation and actin filaments formation are accumulated. Akap4 null sperm also displayed changes of sperm proteome at lesser extends. These results suggest that both AKAP3 and AKAP4 are essential for the formation of sperm sub-cellular structures, proper regulation of PKA activity and motility of sperm, providing new clues to elucidate the molecular pathways that underlie the coordinated synthesis and organization of sperm proteome and sperm morphology

2020-01-14 | PXD016928 | Pride

Low paternal dietary folate alters the sperm epigenome and is associated with negative pregnancy outcomes

Project description:Epidemiological studies suggest that a fatherâ€™s diet can influence offspring health. A proposed mechanism for paternal transmission of environmental information is via the sperm epigenome. The epigenome includes heritable information such as DNA methylation. We hypothesized that the dietary supply of methyl donors would alter epigenetic reprogramming in sperm. This hypothesis was examined by feeding male mice a folate deficient (FD) and folate sufficient (FS) diets and then generating and analyzing DNA methylation profiles of their sperm. C57BL/6 males were fed either the FS or FD diet throughout life (FS, n=32; FD, n=35; 2-3 month old). Pooled gene promoter DNA methylation profiles were generated from the sperm of three FS males and four FD males using the method of MeDIP (Methylated DNA Immunoprecipitation) followed by microarray hybridization.

2013-11-02 | E-GEOD-52017 | biostudies-arrayexpress

Analysis of the honeybee sperm proteome using MudPit and 2D PAGE

Project description:Honeybee semen was collected by gently squeezing the male abdomens. Samples were pooled and then centrifuged. Pelleted sperm was collected and analysed with both 2D PAGE and gel-free methods. For the 2D PAGE, protein spots were digested using trypsin. Extracted peptides, resolved on a C18 column, were analysed by an Agilent LC/MSD Trap XCT Ultra 6330 mass spectrometer. Spectra were searched against the honeybee protein sequences (RefSeq release 48) using Mascot algorithm (with 1 missed cleavage, Cys-carbamidomethylation as fixed modification, and Met-oxidation and N/Q-deamidation as variable modifications). For the MudPit analysis the sperm sample was digested by trypsin. Peptides were resolved using strong cation exchange chromatography followed by reverse phase (C18) HPLC and finally analysed by an Agilent QTOF mass spectrometer. Resulting spectrum files were converted to mzXML and merged using ProteoWizard msconvert. These were then searched against honeybee protein sequences using Mascot, Omssa and X!tandem (all with 1 missed cleavage, and Met-oxidation and N/Q-deamidation as variable modifications). Results of the three search engines were pooled using TPP.

2020-01-17 | PXD000169 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: SWATH quantitation of Seminal Plasma proteins

Project description:Breeding schemes for meat production in rabbits involved a three-way cross of specialized lines in which a paternal line inseminates maternal crossbred females. Paternal line or terminal sire are selected for growth traits, being the males used for the production of fertile dose at the insemination centres and farms. So high growth rate males must produce, in addition, semen in sufficient quantity and quality to meet the demand of insemination and, nevertheless, several studies have been showed that selection for growth have effects on reproduction performance in female and males. In rabbits, negative effects has been observed in ovulation induction, prenatal survival and genetic correlation to fertility. Many factors influence the production and quality of rabbit semen, management as collection frequency, environment (season or photoperiod, nutrition and genetic. Most of the previous studies have been focused in the effects of selection on the seminal and sperm parameters but, little attention has been paid to the protein seminal plasma or sperm composition and if these changes could be affect the fertility of seminal doses obtained from the paternal males. The aim of this study was to evaluate if selection program by daily gain in fattening period has changed seminal traits, plasma and sperm proteoma and, the fertility of semen when it is used in artificial insemination. To do this we uses two re-derived groups of paternal males obtained from vitrified embryos with a difference of 18 generations between both groups.

2020-01-13 | PXD015517 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: Seminal Plasma Spectral Library

2020-01-13 | PXD015511 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: SWATH quantitation sperm membrane proteins

2020-01-13 | PXD015516 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: spermatozoon membrane proteins Spectral Library

2020-01-13 | PXD015510 | Pride

Proteomic analysis of Tmem232-/- and wild type mice sperm

Project description:The sperm were harvested from caudal epididymides of 8-week-old Tmem232-/- and wild-type adult male mice, and subjected to LC-MS/MS analysis.The total proteins of 5,199 were identified and 4,380 of them were quantified. Results showed that 385 differentially expressed proteins were identified including 88 up-regulated and 255 down-regulated genes (Fold Change≥1.5, P<0.05), and group comparisons were presented in a volcano plot.

2024-11-15 | PXD052758 | 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