Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profile of patients affected by Metachromatic Leukodystrophy (MLD)

ABSTRACT: The genome-wide analysis of T lympocytes from 24 MLD patients and a corresponding number of matched controls reveals a list of differentially expressed genes that can be used to build classifiers that correctly classify not only patients and controls with high sensitivity and specificity, but also MLD patients into early- and late-onset clinical classes. Among the most differentially expressed genes, the class of metallothioneins shows a consistent and significant over-expression, confirmed also in affected tissues of patients and mouse models of MLD and other Lysosomal Storage Disorders, indicating metallothioneins a novel dynamic biomarker of disease progression and treatment response in this class of diseases. Moreover, gene onthology analysis performed on the microarray data suggest an involvement of stress response- and autophagy-related pathways as pathological mechanisms in MLD. Total RNA extracted from T-lymphocytes of 24 MLD patients and 24 age-and sex-matched controls

ORGANISM(S): Homo sapiens

SUBMITTER: Martina Cesani

PROVIDER: E-GEOD-23350 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

TRANSCRIPTOME MODIFICATIONS IN HUMAN GINGIVAL FIBROBLASTS EXPOSED TO 2-HYDROXYETHYL-METHACRYLATE (HEMA)

Project description:Objective: 2-Hydroxyethyl methacrylate (HEMA), one of the most common components of tooth filling materials, could diffuse throughout dentine, and in gingival and pulp cells, affecting odontoblast vitality. Design: the aim of this study was to assess the differential transcriptome modulation induced by HEMA treatment in human cultured gingival fibroblasts (HGFs) at different exposure time compared to untreated cells. Materials and methods: Gene expression profile was performed by employing a whole gene microarray approach on RNA extracted from cultured HGFs exposed to 3 mmol/l HEMA for 24 or 96 h. Differentially identified transcripts were analyzed by Ingenuity Pathways Analysis software to disclose genes biological functions. Results: Hierarchical clustering analysis of the data set originated from a total of 8 experiments showed the selective presence of two gene clusters, composed by hundreds trandcripts differentially expressed after 24-h and 96-h HEMA treatment. when compared to untreated controls. Functional analysis showed the transcripts involvement mainly in cell survival, proliferation and death, with an unbalance towards cell growth and inflammatory response. Conclusions: Data analysis showed an overall damage induced by HEMA exposure for both HGFs cultures at 24 and 96-h mainly leading to a proliferation impairement. Interestingly 24-h HEMA exposure could induce the cells to trigger repair mechanisms evidencing an early compensatory response and survive while. 96-h incubation might increase apoptosis as a consequence of the chronic damage. Gene expression profile of Human Gingival Fibroblasts (HGFs) exposed to 3mM 2-Hydroxyethyl Methacrylate (HEMA) for 24- and 96-h versus untreated Human Gingival Fibroblasts at 24- and 96-h. A total of 8 experiments was carried out including biological and technical replicates.

2014-12-15 | E-GEOD-61043 | biostudies-arrayexpress

miRNA expression signatures for human stomach biopsy samples, H. pylori positive versus negative

Project description:We have employed whole microRNA microarray with the potential to distinguish H.pylori infection.Among the 470 human miRNAs represented on the array chip, 228 were undetectable or expressed below the background and so were eliminated, leaving 242 miRNAs for the supervised analysis. When comparing 10 H. pylori-negative and nine H. pylori-positive subjects, 55 miRNAs were deemed significantly different on the basis of microRNA arrays. During endoscopy, a biopsy specimen was obtained from the gastric antrum along the lesser curvature. Biopsies of 10 H. pylori-negative and nine H. pylori-positive patients' subjects were performed.Exclusion criteria were: age <18 or >80 y, pregnancy, body mass index (BMI) >30 kg/m2, diabetes mellitus, cachectic state (including cancer), systemic infection, liver disease, renal impairment, use of medications effective against H. pylori during the preceding 3 months, alcohol abuse, drug addiction, and chronic corticosteroid or nonsteroidal anti-inflammatory drug use. None of the subjects had undergone gastrointestinal surgery.

2010-05-16 | E-GEOD-19769 | biostudies-arrayexpress

A Long Noncoding RNA Acts as a Tumor Promoter in Hepatocellular Carcinoma

Project description:Many long noncoding RNAs are involved in cancer development and progression. Here, we utilized high-throughput microarray to compare the expression difference of transcriptome between the LINC01225 stable knockdown SMCC7721 cells and mock empty plasmid treated SMCC7721 cells; the LINC01225 stable knockdown MHCC97H cells and mock empty plasmid treated MHCC97H cells. These altered genes are involved in tumorigenesis through diverse mechanisms. The present study reveals that LINC01225 functions as a tumor promoter in Hepatocellular Carcinoma. LINC01225 stable knockdown cells were compared to mock empty plasmid treated cells. In addition expression of genes in untreated SMCC7721 cells was detected, we performed a comparison between mock empty plasmid treated SMCC7721 cells and untreated SMCC7721 cells to determine that no confounding factors were brought in. The Agilent human lncRNA+mRNA Array V4.0 were used to perform the analysis.

2017-01-14 | E-MTAB-3833 | biostudies-arrayexpress

Td multispecies interactions

Project description:We utilized T. denticola as a model red complex organism to help determine whether red complex organisms can respond to one another upon cell-cell contact in mixed culture and the types of genes involved in such responses. We extracted RNA from combinations of T. denticola with either other P. intermedia, S. sanguinis, S. gordonii, F. nucleatum, P. gingivalis, or T. forsythia that had been centrifuged to induce cell contact, and identified the numbers and types of genes that were differentially regulated using microarrays.

2013-08-10 | E-MEXP-3059 | biostudies-arrayexpress

Transcription profiling by array of Treponema denticola in response to environmental stresses

Project description:Whole genome expression profiles in response to different suspected stresses including heat, hypo-tonic conditions, oxygen and blood exposure were examined.

2010-08-01 | E-MEXP-2656 | biostudies-arrayexpress

Gene expression of inflammatory monocytes/macrophages after ablative radiotherapy in pancreatic adenocarcinoma

Project description:Ablative RT results in increased expression of CCL2 within the tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC) and also increased recruitment of CD45+CD11b+Ly6Chi inflammatory monocytes/macrophages. This increase in CCL2 expression and recruitment of inflammatory monocytes/macrophages is a mechanism of resistance to the anti-tumor effects of ablative radiotherapy (RT). We used microarrays to study changes in gene expression patterns of inflammatory monocytes/macrophages sorted from the tumor microenvironment after ablative RT in a subcutenous model of pancreatic adenocarcinoma. From this, we identified 8 genes with an absolute fold change of expression equal to or greater than 2 with a false discovery rate equal to or less than 25 %. A pancreatic cancer tumor cell line derived from spontaneously arising tumors in KrasLSL-G12D/+, Trp53LSL-R172H/+, Pdx1-Cre (KPC) mice was subcutaneously implanted into 8 week old female C57BL/6 and allowed to grow for 14 days. After 14 days, 4 mice received 20 Gy of radiation, and 4 mice received a sham treatment. One day post treatment, tumors were harvested, and inflammatory monocytes/macrophages were isolated using flow sorting based on a surface expression phenotype of CD45+ CD11b+ Ly6Chi. From this cell population, total RNA was extracted for creation of cDNA and hybridization on Affymetrix microarrays. From the microarrays, a set of genes associated with radiation treatment of PDAC was identified.

2016-08-01 | E-GEOD-82276 | biostudies-arrayexpress

GATA-1-regulated erythroid microRNAs

Project description:We employed a gene complementation strategy combined with microarray screening to identify miRNAs involved in the formation of erythroid (red blood) cells. To search for GATA-1-regulated erythroid miRNAs, we used the Gata-1– erythroblast line G1E. These cells proliferate in culture as immature erythroid precursors and undergo terminal maturation when GATA-1 activity is restored. G1E-ER4 is a sub-line stably expressing an estrogen-activated form of GATA-1 (GATA-1 fused to the ligand binding domain of the estrogen receptor). Treatment of G1E-ER4 cells with estradiol induces a GATA-1-regulated program of gene expression with concomitant cellular maturation. We used a microarray to evaluate the expression of 292 different miRNAs in G1E-ER4 cells at 0 versus 24 hours after GATA-1 activation. Affymetrix gene expression profiling has previously been deposited (GEO accession no. GSE628). Keywords: microRNA analysis of a cell-line model of erythroid maturation Two condition experiment, 3 replicates each (independently grown and harvested) of untreated and estradiol-treated (24hrs) G1E-ER4 cells, which express an estrogen-responsive form of the GATA-1 transcription factor. Each sample is compared to a common reference sample, comprised of an equal mixture of all 6 experimental samples.

2008-02-05 | E-GEOD-10134 | biostudies-arrayexpress

Fn multispecies biofilm experiment

Project description:This study was conducted to identify whether F. nucleatum has species or group specific transcriptional responses by analyzing dual species biofilms containing either early or late colonizers and utilizing microarrays to identify altered gene expression of F. nucleatum.

2011-11-30 | E-MEXP-3058 | biostudies-arrayexpress

Klinefelter Syndrome testicular gene expression profile by a whole genome microarray approach.

Project description:Objective: Klinefelter Syndrome (KS) is the most common sexual chromosome abnormality (47,XXY) and represents the first genetic cause of male infertility. The mechanisms leading to KS testis degeneration are still unclear and no therapy is so far available for affected patients. The present study is aimed to unravel information about molecules playing a key role in the disruption of the spermatogenesis. Design: Gene expression profiles analysis of KS azoospermic testis versus normal testis, could provide useful information about the molecular basis of the alteration of the spermatogenesis. Materials and Methods: Transcriptome analysis was performed carrying out gene expression profile by a whole genome microarray approach on testis biopsies obtained from 6 azoospermic non-mosaic KS men and from 3 controls, for a total of 12 experiments. T-test and False Discovery Rate were used to evaluate differentially expressed genes. Identified transcripts were analysed by Ingenuity Pathways Analysis software to disclose genes biological functions. Results: Data analysis revealed the differentially up- and down-expression, in KS testis versus the control ones, of 656 and 247 genes related to Endocrine system development and function, Lipid metabolism, Reproductive disease, Free radical scavenging, and Cell death. Conclusions: Take together these data show the presence of several genes involved in testis microenvironment deregulation leading to the spermatogenesis failure. This information, associated with an early diagnosis could help to unravel possible therapeutic targets for testis failure prevention and limitation. Gene expression profile of 6 azoospermic KS testicular biopsies versus 3 pooled control testicular biposies form patients with normal spermatogenesis. A total of 12 experiments was carried out including biological and technical replicates.

2014-06-15 | E-GEOD-54023 | biostudies-arrayexpress

Brucella melitensis global gene expression

Project description:In this study we report that B. melitensis at the late logarithmic phase of growth are more invasive for HeLa cells than at mid logarithmic or stationary growth phases. Microarray analysis of B. melitensis gene expression identified 414 up- and 40 down-regulated genes in late-log growth phase compared to the stationary growth phase. The vast majority of the up-regulated genes in late-log cultures were those associated with DNA replication, transcription and translation, intermediate metabolism, energy production and conversion, membrane transport and cell envelope, biogenesis and outer membrane, while the down-regulated genes were distributed among several functional categories. This first Brucella global gene expression study provides novel information on growth phase-specific gene regulation important not only for understanding Brucella physiology but also the initial molecular interactions between Brucella and its host. Keywords: Comparison bacterial growth phase normalized to genomic DNA There are two kind of samples consisting of RNA isolated from Brucella melitensis grown logarithmically or at stationary phase. There are four biological replicates of each sample. Every Brucella melitensis open reading frame was printed in triplicate on each microarray, thereby providing three technical replicates for each biological replicates. Each replicate was normalized against labeled Brucella melitensis genomic DNA.

2010-05-19 | E-GEOD-11192 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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