Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Galactosylceramide impact on male and female Cln3Δex7/8 mouse brain gene expression

ABSTRACT: The purpose of this study is to discern global expression programs embodying therapeutic targeting of CLN3 disease. Differential gene expression in Cln3Δex7/8 mouse brains was determined after intraperitoneal vehicle/Galactosylceramide (GalCer) injections, for 40 weeks, using GeneChip Mouse Genome 430 2.0 arrays. Differentially expressed genes among Cln3Δex7/8 mice and profiles modulated by GalCer treatment were functionally analyzed and topologically organized.

ORGANISM(S): Mus musculus

SUBMITTER: Joelle Makoukji

PROVIDER: E-MTAB-9232 | 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

Gene expression profiling of human whole-blood samples before and after the administration of recombinant human erythropoietin

Project description:As part of cross-platform comparisons of microarray and RNA-seq, this current experiment using the Affymetrix Human Transcriptome Array 2.0 aimed to quantify gene-level expression in subjects administered recombinant human erythropoietin over a 10-week protocol for the identification of gene signatures of blood doping. These results were compared to results obtained from other gene expression quantification platforms using the same experimental cohort, including the Illumina HumanHT-12v4 Expression BeadChips (archived in ArrayExpression; E-MTAB-2874), Illumina NextSeq 500 and MGI DNBSEQ-G400RS.

2021-11-04 | E-MTAB-11080 | biostudies-arrayexpress

Transcritional profiling in 30 follicular cell derived thyroid cancers

Project description:We established transcriptional profiles by microarray in a small series of follicular cell derived thyroid cancers collected at our Institute. This series comprises 27 papillary thyroid carcinomas (PTCs), the most common type of thyroid cancer, and 3 poorly differentiated thyroid carcinomas (PDTCs). Two patient matched non-neoplastic thyroids are also included as controls.

2024-07-27 | E-MTAB-13222 | biostudies-arrayexpress

Gene expression analyses in male and female Cln3Δex7/8 mouse brains following oral administration of flupirtine for 14 weeks

Project description:The Neuronal Ceroid Lipofuscinoses, one of the most common fatal neurodegenerative diseases of childhood, is caused by mutations of the CLN3 gene. Treatment regimens are symptomatic, highlighting the importance of disease-modifying drugs. Flupirtine confers neuroprotective effects in CLN3-deficient cells as well as in Cln3Δex7/8 mice. The purpose of the present study is to discern global expression programs embodying therapeutic targeting of CLN3 disease. Differential gene expression in the brains of 18-week-old Cln3Δex7/8 mice, a knock-in mouse model, was determined after daily oral supplementation of vehicle or flupirtine (30 mg/kg BW), for a period of 14 weeks, using GeneChip Mouse Genome 430 2.0 array platform from Affymetrix and quantitative real-time PCR. This manuscript sheds light on global expression programs that are associated with therapeutic treatment of CLN3 disease by flupirtine in male and female mice separately. Understanding the molecular effects of flupirtine treatment herein would pave the way for new personalized and sex-specific strategies for treatment of this debilitating genetic disease.

2021-05-01 | E-MTAB-9812 | biostudies-arrayexpress

Circadian 45h time-course RNA-seq expression profiling of HCT116 cells in WT condition and upon CRISPR/Cas9-mediated knock-out of core-clock genes ARNTL, PER2 and NR1D1

Project description:A 45h time-course RNA-seq study was performed to analyse the different circadian phenotypes of human colorectal cancer cell line HCT116 WT, HCT116 ARNTL Knockout, HCT116 PER2 Knockout and HCT116 NR1D1 Knockout cells. Samples were taken every 3h starting from 9h after cell synchronization for a period of 45h resulting in 16 time-points for each cell line.

2022-04-30 | E-MTAB-9701 | biostudies-arrayexpress

Mutant p53R273H regulated microRNA profiling in presence and absence of DNA damage in H1299 cells

Project description:In the present study, we used a high-throughput small RNA deep sequencing followed by a systematic computational analysis to identify genome wide mutant p53R273H regulated miRNAs in both DNA damage dependent and independent context. Several miRNA-mRNA regulatory networks have been predicted that might contribute to mutant p53 GOF properties. Differentially regulated miRNA signature profile has been validated in the lung cancer patients harboring wildtype and mutant p53. We identified specific miRNA signatures for lymph node metastasis associated with p53 mutation in lung adenocarcinoma and also predicted the possible contribution of two mutant p53 regulated miRNAs in EMT process. Furthermore, this study identified a hitherto unknown miRNA in human which might act as one of the crucial downstream targets of GOF mutant p53 to confer oncogenic properties. Determination of mutant p53R273H regulated microRNAs H1299 cells.

2017-04-28 | E-GEOD-68353 | biostudies-arrayexpress

The whole transcriptome changes in melanoma cells under dacarbazine treatment

Project description:The experiment was performed to reveal transcriptomic alterations in melanoma cells caused by dacarbazine (DTIC) treatment. Two primary cell cultures were exposed to dacarbazine at a final concentration of 1 mg/mL. The whole transcriptome was investigated in the cells treated with DTIC compared to a negative control group.

2021-04-09 | E-MTAB-10359 | biostudies-arrayexpress

miRNA sequencing of rat hearts treated chronically with rofecoxib or its vehicle

Project description:We reported previously that chronic treatment with the Cyclooxygenase-2 inhibitor, rofecoxib, increased acute mortality in rats exposed to ischemia/reperfusion injury (I/R). This manifestation of hidden cardiotoxicity was attributed to the proarrhythmic effect of the drug on the ischemic heart. However, rofecoxib also had beneficial effects on ischemic injury, manifesting as decreased infarct size. In the present study, we aimed to identify molecular changes caused by chronic rofecoxib treatment in the heart. Rats were treated with 5.12 mg/kg rofecoxib or its vehicle for four weeks. Messenger RNA (mRNA), microRNA (miRNA) deep sequencing data, and proteomic datasets of left ventricular tissue samples were used for an unbiased differential expression analysis followed by in silico molecular network analysis and experimental target validation. Using mass spectrometry and filtering criteria, 26 proteins were identified that exhibited pronounced changes in protein expression or phosphorylation due to chronic rofecoxib treatment. The transcriptomic analysis showed mild alterations in the heart´s mRNA- and miRNA expression. The posttranscriptional regulation of mRNAs by miRNAs did not result in differential protein expression. This is the first demonstration that chronic rofecoxib treatment affects posttranslational modification and expression of several proteins in the heart. These are potential off-target effects that could account for the hidden cardiotoxic and/or cardioprotective effects of rofecoxib.

2024-10-30 | E-MTAB-13909 | biostudies-arrayexpress

Targeted inhibition of ubiquitin signaling reverses the metabolic reprogramming and suppresses Glioblastoma growth

Project description:Glioblastoma (GBM) is the most frequent and aggressive form of primary brain tumor in the adult population, and the high recurrence rate and resistance to current therapeutics urgently demand a better therapy for this disease. Regulation of protein stability by the ubiquitin proteasome system (UPS) represents an important control mechanism of cell growth. Deregulation of UPS is mechanistically linked to the development and progression of a variety of human cancers, including GBM. Thus, UPS system represents a valuable target for GBM treatment. Here, we find that the E3 ligase praja2 selectively marks primary IDH1-wild type GBM. By using an integrated approach, including proteomics, transcriptomics and metabolic profiling, we identify praja2 as a main component of a signaling network that regulates cancer cell growth and metabolism. We show that praja2 binds and regulates the stability of the Kinase Suppressor of Ras 2 (KSR2) and as consequence, the activity of the downstream AMP-dependent protein kinase (AMPK) in GBM cells. By degrading KSR2, praja2 attenuates the oxidative metabolism and promotes the aerobic glycolysis (Warburg effect). Brain delivery of siRNAs targeting praja2 upregulates KSR2 and negatively impacted on GBM growth, reducing the tumor size and significantly improving the survival rate of treated mice. These data highlight the role of praja2 as an essential regulator of cancer cell metabolism, and as a preferential therapeutic target to suppress GBM growth

2022-06-29 | E-MTAB-11137 | biostudies-arrayexpress

Transcriptional profiles of NRAS- and BRAF-mutant melanoma cell lines under normal conditions and in response to glucose starvation

Project description:NRAS and BRAF are the most commonly found genetic alterations in melanoma. It has been demonstrated that NRAS and BRAF oncogenic alterations, even affecting the same signaling pathway, represent two different clinical and biochemical entities, showing different signaling patterns and biological responses. Metabolic reprogramming is considered a novel target to control cancer; however, it is mostly unknown how the NRAS oncogene contributes to this cancer hallmark. We have showed that NRAS-mutated melanomas harbor specific metabolic alterations that render cells sensitive to RAS pathway inhibition upon metabolic stress. Gene expression analysis has confirmed different transcriptional profiles of NRAS- and BRAF- mutant cells both, under basal conditions and in response to glucose starvation. Moreover, analysis of glucose metabolism-related genes expression regulation revealed PFKFB2 as an important player linking glycolysis and RAS pathway activation.

2022-08-31 | E-MTAB-10921 | 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