Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk transcriptomic profiles of mouse testes in response to male environmental exposures across age and genetic background

ABSTRACT: This study includes raw data of testis RNA-seq profiles from treated (nABX & LPHS, with nABX: non-absorbable antibiotics and LPHS: low-protein, high sugar diet) and control (CON) males of mature (57-62 weeks) and young (9-11 weeks) FVB & C57BL/6J backgrounds. Sequencing was done using 40bp paired-end reads on a NextSeq500 sequencer, obtaining an average of 25 million reads per sample.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-14638 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Bulk transcriptomic profiles of mouse testes in response to male environmental exposures in the young FVB background

Project description:This study includes raw data of testis RNA-seq profiles from treated (nABX & LPHS, with nABX: non-absorbable antibiotics LPHS: low-protein, high sugar diet) and control (CON) males of young (10-11 weeks) FVB background. Sequencing was done using 40bp paired-end reads on a NextSeq500 sequencer, obtaining an average of 25 million reads per sample.

2024-11-22 | E-MTAB-14637 | biostudies-arrayexpress

Small RNA profiles of mouse sperm in response to male environmental exposures across age and genetic background

Project description:This study includes raw data of sperm smallRNA profiles from treated (nABX & LPHS, with nABX: non-absorbable antibiotics ; LPHS: low-protein, high sugar diet) and control (CON) males across FVB and C57BL/6J genetic backgrounds and mature (76-78 weeks (>1yr)) and young (10-11 weeks) ages. Sequencing was conducted at 100 bp, single-end on a Nextseq2000, resulting in approximately 1-5 million reads for most samples.

2024-11-22 | E-MTAB-14636 | biostudies-arrayexpress

Single-embryo transcriptomic profiles of mouse blastocysts in response to paternal environmental exposures in young C57BL/6J background

Project description:This study includes raw data of blastocyst single-embryo SMART-seq profiles generated by IVF using sperm derived from treated (nABX & LPHS with nABX: non-absorbable antibiotics and LPHS: low-protein, high sugar diet) and control (CON) males of young (9-11 weeks) C57BL/6J background. After SMART-seq library preparation of single embryos, indexed samples were pooled and sequenced on the NextSeq 2000 using a P3 flow cell in 50bp paired-end mode, targeting an average of 5 million reads per sample.

2024-11-22 | E-MTAB-14639 | biostudies-arrayexpress

Single-embryo transcriptomic profiles of mouse blastocysts in response to paternal environmental exposures in young FVB background

Project description:This study includes raw data of blastocyst single-embryo SMART-seq profiles generated by IVF using sperm derived from treated (nABX & LPHS, with nABX: non-absorbable antibiotics and LPHS: low-protein, high sugar diet) and control (CON) males of young (9-10 weeks) FVB background. After SMART-seq library preparation of single embryos, indexed samples were pooled and sequenced on the NextSeq 2000 using a P3 flow cell in 50bp paired-end mode, targeting an average of 5 million reads per sample.

2024-11-22 | E-MTAB-14640 | biostudies-arrayexpress

In-depth proteomic analysis of nasal fluids from patients with chronic rhinosinusitis and nasal polyps by data-independent acqusition

Project description:Antibiotics are commonly prescribed to treat chronic rhinosinusitis (CRS). However, the effects of antibiotics on the microbiome and secreted proteome remain unknown in regard to CRS.We analyzed the effects of antibiotics on the nasal secreted proteome inthe context of CRS using data-independent acqusition proteomics approach.

2021-09-09 | PXD018960 | Pride

Persistent chromatin modifications induced by high fat diet

Project description:Obesity is a highly heritable complex disease that results from the interaction of multiple genetic and environmental factors. Formerly obese individuals are susceptible to metabolic disorders later in life, even after lifestyle changes are made to mitigate the obese state. This is reminiscent of the metabolic memory phenomenon originally observed for persistent complications in diabetic patients, despite subsequent glycemic control. Epigenetic modifications represent a potential mediator of this observed memory. We previously demonstrated that a high fat (HF) diet leads to changes in chromatin accessibility in the mouse liver. The regions of greatest chromatin changes in accessibility are largely strain dependent, indicating a genetic component in diet-induced chromatin alterations. We have now examined the persistence of diet-induced chromatin accessibility changes upon diet reversal in two strains of mice. We find that a substantial fraction of loci that undergo chromatin accessibility changes with HF diet remain in the remodeled state after diet reversal in C57BL/6J mice. In contrast, the vast majority of diet-induced chromatin accessibility changes in A/J mice are transient. Our data also indicate that the persistent chromatin accessibility changes observed in C57BL/6J are associated with specific transcription factors and histone posttranslational modifications. The persistent loci identified here are likely to be contributing to the overall phenotype and are attractive targets for therapeutic intervention. Examination of chromatin remodeling with FAIRE-seq in livers of C57BL/6J and A/J mice on three diet regimen: 1) control diet for 16 weeks, 2) high fat diet for 16 weeks, or 3) high fat diet for 8 weeks with control diet for 8 weeks. These chromatin profiles were complemented with gene expression data (RNA-seq)

2016-03-22 | E-GEOD-75984 | biostudies-arrayexpress

A preclinical mouse model of nonalcoholic steatohepatitis and hepatocellular cancer that mimics human disease

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-07-25 | E-GEOD-67680 | biostudies-arrayexpress

Effects of Iron Deficiency and Risperidone treatment on the rat frontal cortex

Project description:Prenatal iron deficiency (pID) has been described to increase the risk for neurodevelopmental disorders such as autism and schizophrenia; however, the precise molecular mechanisms are still unknown. Here, we utilized high throughput mass spectrometry to examine the proteomic effects of pID in adulthood on the rat frontal cortex area (FCA). In addition, the FCA proteome was examined in adulthood following risperidone treatment in adolescence to see if these effects could be prevented. We identified 1501 proteins of which 100 were significantly differentially expressed in the FCA at post-natal day 90. Pathway Analysis of proteins affected by pID revealed changes in metabolic processes, including the tricyclic acid cycle, mitochondrial dysfunction, and P13K/Akt signaling. Interestingly, most of these protein changes were not present in the adult pID offspring who received risperidone in adolescence. Behavioral testing of pID rats demonstrated social impairment and poor performance during novelty-induced exploration in pID animals in line with a abnormal neurodevelopmental phenotype. Considering the link between prenatal iron deficiency and several neurodevelopmental disorders such as autism and schizophrenia these presented results bring new perspectives to understand the role of iron in metabolic pathways and provide novel biomarkers for future studies of prenatal iron deficiency.

2018-07-05 | PXD004975 | Pride

Proteomic detection of mouse liver

Project description:This study aimed to investigate the mechanism of SYT on lipid metabolism and insulin sensitivity in high-fat diet (HFD)-induced obese mice by means of combining lipidomics and proteomics. The obese mice models were developed via HFD feeding for 20 consecutive weeks. Mice in the treatment group were given metformin and SYT respectively, and the effects of SYT on body weight, blood glucose, insulin sensitivity, fat accumulation in the organs, and pathological changes in the liver were monitored. Lipid metabolism was examined by lipidomics. Further determination of signaling pathways was detected by proteomics. The biological contributions of the compounds detected in SYT's chemical fingerprint were predicted by network pharmacology. Overall, our study provides supportive evidence for the mechanism of SYT's therapeutic effect on dysregulated lipid metabolism in diabesity.

2022-02-15 | PXD028317 | Pride

Mechanisms of Stable Lipid Loss in a Social Insect

Project description:Effects of behavioral maturation, diet quality and Queen Mandibular Pheromone on gene expression in the abdominal fat bodies of worker honey bees.

2011-07-01 | E-MTAB-495 | 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