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

Clariom S mouse arrays of C57Bl6/NTac mice to analyse how obesogenic diet exposure of parents induces sex-specific programming of overweight in mouse offspring

ABSTRACT: The arrays were used to explore how parents’ obesity status influence their offspring’s weight. We randomly assigned three-week-old mice to two groups, one group receiving a high-fat diet (HFD), the other group receiving a control diet (chow). Adult females of both groups were mated to males fed with HFD or CD. F1 transcriptome assay data were created from four tissues (liver, epigonal visceral, inguinal subcutaneous, and interscapular brown adipose tissue) of male offspring in relation to their parents’ obesity status.

ORGANISM(S): Mus musculus

SUBMITTER: Anne Hoffmann

PROVIDER: E-MTAB-13493 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A phase II trial of weekly nab-paclitaxel for progressive and symptomatic desmoid tumors

Project description:The uploaded datasets contains raw data from our research: columns represent patients, rows represent meta data (patients response, type of sarcoma, etc ...) + the raw gene counts.

2022-09-01 | E-MTAB-12163 | biostudies-arrayexpress

microarray of healthy heart tissue of mouse (BALB/c nude female mice) after proton-beam treatment to cure breast cancer

Project description:Proton irradiation: 2, 6 and 9 Gy + untreated controls Times after irradiation: 3 and 10 days Associated pubblication: Sala, C.; Tarozzi, M.; Simonetti, G.; Pazzaglia, M.; Cammarata, F.P.; Russo, G.; Acquaviva, R.; Cirrone, G.A.P.; Petringa, G.; Catalano, R.; et al. Impact on the Transcriptome of Proton Beam Irradiation Targeted at Healthy Cardiac Tissue of Mice. Cancers 2024.

2024-04-30 | E-MTAB-14006 | biostudies-arrayexpress

Human Illumina 850K EPIC methylation arrays of blood, subcutaneous and omental visceral adipose tissue from two-step surgical approach

Project description:Genome wide DNA methylation in blood, subcutaneous and omental visceral adipose tissue from two-step surgical approach (N=9) was analysed in patients with severe obesity using Illumina 850K EPIC technology before and after metabolic surgery (Leipzig Obesity BioBank (LOBB) cohort). Additionally, a validation blood cohort of patients with obesity undergoing metabolic surgery was analyzed for results validation.

2024-03-31 | E-MTAB-13564 | biostudies-arrayexpress

Transcription profiling of hepatic response to anti-diabetic drug and dietary lifestyle interventions in LDLR-/- mice

Project description:Lean male mice were fed a high fat diet (HFD, lard 24% w/w) for 16 weeks. At 9 weeks, when all hallmarks of prediabetes were established, groups of mice were treated with drug (metformin, glibenclamide, sitagliptin, rosiglitazone, pioglitazone, fenofibrate, T0901317, atorvastatin, salicylate or rofecoxib) for another 7 weeks together with the high fat diet. An additional group was switched back to a chow diet (dietary lifestyle intervention) after the first 9 weeks of high fat diet. All groups were compared to a control group receiving HFD alone and to a reference group fed chow (baseline reference) for the entire experimental period (16 weeks).

2013-04-18 | E-MTAB-1063 | biostudies-arrayexpress

Delayed Cardiomyocyte Response to Total Body Particle Radiation Exposure â Identification of Regulatory Gene Network [proton]

Project description:We examined molecular responses using transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) proton (56Fe) particles 1, 3, 7, 14 and 28 days after exposure. Unsupervised clustering analysis of gene expression segregated samples according to the radiation (IR) response, and time after exposure with 56Fe-IR showing the greatest level of gene modulation. 1H-IR exposures showed little differential transcript modulation. Network analysis categorized the major differentially expressed genes into cell cycle, oxidative responses and transcriptional regulation functional groups. Transcriptional networks identified key nodes regulating expression. Individual transcription factors were inferred to be active at 1, 3, 7, 14 and 28 days after exposure. Validation of the signal transduction network by protein analysis showed that particle IR clearly regulates a long lived signaling mechanism for p38 MAPK signaling and NFATc4 activation. Electrophoresis mobility shift assays supported the role of additional key transcription factors GATA-4, STAT-3 and NF-ÎºB as regulators of the response at specific time points. These data suggest that the molecular response to 56Fe-IR is unique and shows long-lasting gene expression in cardiomyocytes, up to 28 days after exposure. Additionally, proteins involved in signal transduction and transcriptional activation via DNA binding play a role in the response to high charge (Z) and energy (E) particles (HZE). Our study may have implications for NASAâs efforts to develop heart disease risk estimates for astronauts safety via identification of specific HZE-IR molecular markers and for patients receiving conventional and particle radiotherapy. Transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) proton (56Fe) particles 1, 3, 7, 14 and 28 days after exposure.

2016-07-03 | E-GEOD-68875 | biostudies-arrayexpress

Delayed Cardiomyocyte Response to Total Body Particle Radiation Exposure â?? Identification of Regulatory Gene Network [iron]

Project description:We examined molecular responses using transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) iron (56Fe) particles 1, 3, 7, 14 and 28 days after exposure. Unsupervised clustering analysis of gene expression segregated samples according to the radiation (IR) response, and time after exposure with 56Fe-IR showing the greatest level of gene modulation. 1H-IR exposures showed little differential transcript modulation. Network analysis categorized the major differentially expressed genes into cell cycle, oxidative responses and transcriptional regulation functional groups. Transcriptional networks identified key nodes regulating expression. Individual transcription factors were inferred to be active at 1, 3, 7, 14 and 28 days after exposure. Validation of the signal transduction network by protein analysis showed that particle IR clearly regulates a long lived signaling mechanism for p38 MAPK signaling and NFATc4 activation. Electrophoresis mobility shift assays supported the role of additional key transcription factors GATA-4, STAT-3 and NF-ÎºB as regulators of the response at specific time points. These data suggest that the molecular response to 56Fe-IR is unique and shows long-lasting gene expression in cardiomyocytes, up to 28 days after exposure. Additionally, proteins involved in signal transduction and transcriptional activation via DNA binding play a role in the response to high charge (Z) and energy (E) particles (HZE). Our study may have implications for NASAâ??s efforts to develop heart disease risk estimates for astronauts safety via identification of specific HZE-IR molecular markers and for patients receiving conventional and particle radiotherapy. Transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) iron (56Fe) particles 1, 3, 7, 14 and 28 days after exposure.

2016-07-03 | E-GEOD-68874 | biostudies-arrayexpress

Transcription profiling by array of adipose samples from LDLR-/- mice to study response to anti-diabetic drug and dietary lifestyle interventions

Project description:Lean male mice were fed a high fat diet (HFD, lard 24% w/w) for 16 weeks. At 9 weeks, when all hallmarks of prediabetes were established, groups of mice were treated with drug (rosiglitazone, pioglitazone, T0901317, or salicylate) for another 7 weeks together with the high fat diet. An additional group was switched back to a chow diet (dietary lifestyle intervention) after the first 9 weeks of high fat diet. All groups were compared to a control group receiving HFD alone and to a reference group fed chow (baseline reference) for the entire experimental period (16 weeks). One group (n=9) remained on maintenance chow throughout the entire study period (16 weeks) and served as healthy, age-matched control. After the nine week run-in period, the HFD fed mice were matched into thirteen groups based on body weight. The first group (n=9) was sacrificed immediately after matching. The second group (n=15) was continued on HFD until the end of the experiment at t=16 weeks. The fourth group (n=9) was switched to regular chow (dietary lifestyle intervention). The other groups (each n=9) continued on HFD supplemented with drugs typically used in clinical practice. More specifically, following drugs were mixed into HFD ; rosiglitazone (0.010% w/w), pioglitazone (0.010% w/w), T0901317 (0.010% w/w) and salicylate (0.40% w/w).

2014-05-14 | E-GEOD-57659 | biostudies-arrayexpress

Effects of LIFR inhibition using EC359 on TNBC cells in obesity conditions

Project description:In a study using syngeneic BALB/c mice, the impact of a high-fat diet (HFD) on triple-negative breast cancer (TNBC) progression was investigated using 4T1 cells. Mice were fed either a low-fat diet (LFD) or HFD for six weeks before receiving orthotopic injections of 4T1 cells. Post-tumor formation, mice were randomized into three groups: LFD, HFD, and HFD with EC359 treatment. Results indicated that HFD significantly enhanced tumor growth, while EC359 treatment notably reduced HFD-induced TNBC progression. To explore underlying mechanisms, global RNA sequencing was performed on tumor tissues, revealing that HFD altered the expression of 578 genes compared to LFD, with 325 genes differentially expressed between the HFD and HFD + EC359 groups. Gene set enrichment analysis showed that HFD-related genes were linked to cytokine signaling, inflammation, stem cell pathways, TGFβ, metastasis, and epithelial–mesenchymal transition, all of which were downregulated with EC359 treatment.

2024-11-14 | GSE280092 | GEO

Genome-wide RNAseq of liver tissue derived from DEN-CDA-HFD mice treated with CLDN1 mAb or vehicle Control

Project description:Seven-week old male C57BL/6J mice received a single i.p. injection of DEN (100 mg/kg) and were subsequently fed with CDA-HFD after 3 weeks. After 6 weeks of diet, the mice were randomized in 2 groups, receiving weekly i.p. injections of 500 µg of either CLDN1 specific mAb or vehicle control for 16 weeks. RNA was extracted from non-tumorous liver tissue of 6 DEN-CDA-HFD mice treated with CLDN1 mAb, 6 DEN-CDA-HFD mice treated with vehicle Control as well as 5 C57BL/6J Control mice fed by regular diet. Libraries were sequenced on the Illumina HiSeq 4000 as Single-Read 50 base reads.

2024-03-12 | GSE174542 | GEO

Spleen proteomics data from high fat diet fed mice

Project description:The composition of the diet affects many processes in the body, including body weight and endocrine system. We have previously shown that dietary fat also affects the immune system. Mice fed high fat diet rich in polyunsaturated fatty acids survive S. aureus infection to a much greater extent than mice fed high fat diet rich in saturated fatty acids. Here we present data regarding the dietary effects on protein expression in spleen from mice fed three different diets, I) low fat/chow diet (LFD, n=4), II) high fat diet rich in saturated fatty acids (HFD-S, n=4) and III) high fat diet rich in polyunsaturated fatty acids (HFD-P, n=4). We performed mass spectrophotometry based quantitative proteomics analysis of isolated spleen by implementing the isobaric tags for relative and absolute quantification (iTRAQ) approach. Mass spectrometry data were analysed using Proteome Discoverer 2.4 software using the search engine mascot against Mus musculus in SwissProt. 924 proteins are identified in all sets (n=4) for different dietary effects taken for statistical analysis using Qlucore Omics Explorer software. Only 20 proteins were found to be differentially expressed with a cut-off value of false discovery rate < 0.1 (q-value) when comparing HFD-S and HFD-P but no differentially expressed proteins were found when LFD was compared with HFD-P or HFD-S. We identified a subset of proteins that showed an inverse expression pattern between two high fat diets. These differentially expressed proteins were further classified by gene ontology for their role in biological processes and molecular functions.

2020-08-06 | PXD020365 | 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