Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide identification of urinary cell-free microRNAs for non-invasive detection of bladder cancer

ABSTRACT: Objective was to identify urine cell-free microRNAs enabling early non-invasive detection of bladder cancer. Total RNA enriched for fraction of short RNAs was isolated using Urine microRNA purification kit (Norgen corp.). miRNA profiles were determined using the Affymetrix GeneChip miRNA 3.0 array and analyzed to identify differentially deregulated miRNA in bladder cancer patients compared with helathy controls.

ORGANISM(S): Homo sapiens

SUBMITTER: Jaroslav Juracek

PROVIDER: E-MTAB-6102 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

microRNAs as predictive biomarkers of response to sunitinib or pazopanib in patients with metastatic renal cell carcinoma

Project description:The aim of the experiment was to discover differentially expressed miRNAs correlating with prolonged response to targeted therapy in patients with metastatic renal cell carcinoma treated with sunitinib or pazopanib

2018-02-08 | E-MTAB-6296 | biostudies-arrayexpress

microRNA expression profiling of urine and cancer tissues of patients with bladder cancer, and those from the controls with haematuria

Project description:Mid-stream urine was collected from bladder cancer patients prior to surgery. Both tumor tissue and normal bladder mucosa that are located at >3cm away from the tumor edge were obtained by cystoscopy. For the normal controls with haematuria, urine samples were collected from patients who had normal cystoscopic finding and absence of malignancy with >6 months follow-up. All urine samples were centrifuged at 2500 r.c.f. for 20 minutes and the urine supernatant was collected. Total RNA of urine supernatant and frozen tissue was extracted using MirVanaTM PARISTM Kit (Ambion) in accordance with the manufacturerâs recommended protocols. AgilentTM Human miRNA Microarray Chip (Release 13.0, Agilent Technologies, Santa Clara, CA, USA) was used to determine the microRNA expression profiles of the samples.

2014-04-16 | E-MTAB-2573 | biostudies-arrayexpress

Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Cervix samples miRNA]

Project description:Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits ability to expression profile, we explored factors predicting success for FFPE profiling and investigated an approach overcoming this limitation. Methods: Bladder (n=141, stored 3-8 years) and cervix (n=160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon1.0ST arrays. Percent detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. Precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Eight-old and -young cervix samples were compared using Affymetrix miRNA 2.0 arrays. For comparison, the 'cervix_tumour_cs1_113' (previsously submitted GSM677307) was included and re-analyzed with the samples from the current study (total 161 Cervix samples). Results: RNA quality controls (e.g. RNA integrity number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R2=-0.30, p<0.01) and cervix (R2=-0.69, p<0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; p=1.10x10-5). Median miRNA probeset expression of eight-old and eight-young cervix samples correlated well (R2=0.95) overcoming the age-related bias of mRNA probesets, suggesting miR-205 stability generalises across microRNA. Conclusions: microRNA profiling overcomes the limitation of degraded FFPE samples 18 samples hybridised to miRNA microarray V2 arrays, 2 cervix cell lines and 16 clinical cervical tumour samples. There are no technical replicates.

2012-07-03 | E-GEOD-39015 | biostudies-arrayexpress

Differentially Expressed Wound Healing-Related microRNAs in the Human Diabetic Cornea

Project description:MicroRNAs are powerful gene expression regulators, but their corneal repertoire and potential changes in corneal diseases remain unknown. Our purpose was to identify miRNAs altered in the human diabetic cornea by microarray analysis, and to examine their effects on wound healing in cultured telomerase-immortalized human corneal epithelial cells (HCEC) in vitro. Using microarrays, 29 miRNAs were identified as differentially expressed in diabetic samples. Two miRNA candidates showing the highest fold increased in expression in the diabetic cornea were confirmed by Q-PCR and further characterized. HCEC transfection with h-miR-146a or h-miR-424 significantly retarded wound closure, but their respective antagomirs significantly enhanced wound healing vs. controls. Cells treated with h-miR-146a or h-miR-424 had decreased p-p38 and p-EGFR staining, but these increased over control levels close to the wound edge upon antagomir treatment. In conclusion, several miRNAs with increased expression in human diabetic central corneas were found. Two such miRNAs inhibited cultured corneal epithelial cell wound healing. Dysregulation of miRNA expression in human diabetic cornea may be an important mediator of abnormal wound healing. Total RNA was extracted from age-matched human autopsy normal (n=6) and diabetic (n=6) central corneas, Flash Tag end-labeled, and hybridized to Affymetrix® GeneChip® miRNA Arrays. Select miRNAs associated with diabetic cornea were validated by quantitative RT-PCR (Q-PCR) and by in situ hybridization (ISH) in independent samples.

2013-11-09 | E-GEOD-52233 | biostudies-arrayexpress

Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA

Project description:This SuperSeries is composed of the following subset Series: GSE39013: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Cervix samples series 1] GSE39014: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Cervix samples series 2] GSE39015: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Cervix samples miRNA] GSE39016: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Bladder samples] GSE39066: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [cell lines] Refer to individual Series

2012-07-03 | E-GEOD-39067 | biostudies-arrayexpress

miRNA profiling of MCF-7 and MDA-MB-231 breast cancer cells treated or not with phytoestrogen Emodin

Project description:Estrogen receptor positive MCF-7 and estrogen receptor negative MDA-MB-231 breast cancer cells treated with 10µg/ml phytoestrogen Emodin (1,3,8-trihydroxy-6-methylanthraquinone) and their control cells (untreated with Emodin) were incubated for 48 hours. All samples were prepared as duplicates to have biological replicates. Isolated RNA samples were used for miRNA microarray analysis. Through this experiment miRNA profiling of breast cancer cells having estrogen receptor and not were revealed upon phytoestrogen Emodin treatment.

2023-11-30 | E-MTAB-10170 | biostudies-arrayexpress

miRNA expression in lung infiltrating mononuclear cells after exposure to Staphylococcal enterotoxin B

Project description:C57BL/6 mice were either given Staphyloccocal entertoxin B (SEB) or PBS as a control for 48 hours. Mice were sacrificed and lung infiltrating mononuclear cells were isolated. Total RNA extraction was performed using Qiagen miRNeasy kit and RNA quality was assessed specrophotometrically. Affymetric Gene Chip miRNA 1.0 array was used for miRNA profiling using FlashTag Biotin HSR RNA labeling kit.

2014-04-01 | E-MTAB-2379 | biostudies-arrayexpress

Persistence of Smoking-induced Dysregulation of Small Airway Epithelium miRNA Expression Despite Smoking Cessation

Project description:Rationale: Even after quitting smoking, the risk of the development of chronic obstructive pulmonary disease (COPD) and lung cancer remains significantly higher compared to never-smokers. Objectives: Based on the knowledge that COPD and most lung cancers start in the small airway epithelium (SAE), we hypothesized that smoking modulates miRNA expression in the SAE linked to the pathogenesis of smoking-induced airway disease, and that some of these changes persist after smoking cessation. Methods: SAE was collected from 10th to 12th order bronchi using fiberoptic bronchoscopy. Affymetrix miRNA 2.0 arrays were used to assess miRNA expression in the SAE from 10 healthy never-smokers and 10 healthy smokers, before and after they quit for 3 months. Smoking status was determined by urine nicotine and cotinine measurement. Results: There were significant differences in the expression of 34 miRNAs between healthy smokers and healthy never-smokers (p<0.01, fold-change >1.5), with functions associated with lung development, airway epithelium differentiation, inflammation and cancer. After quitting smoking for 3 months, 12 out of the 34 miRNAs did not return to normal levels, with Wnt/Î²-catenin signaling pathway the top enriched pathway of the target genes of the persistent deregulated miRNAs. Conclusions: In the context that many of these persistent smoking-dependent miRNAs are associated with differentiation, inflammation diseases or lung cancer, it is likely that persistent smoking-related changes in small airway epithelium miRNAs play a role in the subsequent development of these disorders. MicroRNA profiling identified 34 miRNAs up-regulated by cigarette smoking in human small airway epithelium. Even after quitting smoking for 3 months, 12 miRNAs didnât return to normal level.

2015-11-23 | E-GEOD-53519 | biostudies-arrayexpress

DamX controls reversible cell morphology-switching in uropathogenic Escherichia coli.

Project description:Transcriptional analysis of UTI89 - uropathogenic E.coli (UPEC) strain grown in urine/Luria bertani medium culture in vitro as well as during three distinct phases of UPEC bladder infection: intracellular growth, filament formation and filament reversal. UTI89 was used to infect a bladder epithelial cell line cultured within a dynamic flow chamber system and harvested at particular stages of its pathogenecity cascade. Total RNA was processed and cy3 labeled for microarray analysis using Agilent custom Escherichia coli UTI89 arrays designed using E-Array.

2017-05-28 | E-MTAB-3611 | biostudies-arrayexpress

microRNA expression of human periodontal ligament derived stem cell line exposed to 1 microMolar (uM) (-)-nicotine liquid or 1 uM nicotine electronic cigarette vapor extract against untreated control

Project description:Nicotine and cigarette smoking have been previously shown to inhibit the differentiation potential and miRNA expression of human periodontal ligament derived stem cells (PDLSCs). Electronic cigarette (EC) vapor also contains nicotine, as well as other non-nicotine compounds, and, like cigarette smoking, EC vaping results in similar routes of toxic exposure for PDLSCs. The effect of exposure on PDLSC miRNA expression is unknown. To determine these effects, cultured PDLSCs were exposed to media supplemented with 1 uM nicotine EC vapor extract for 72h, during which media was changed every 24h. To produce vapor extract, an EC filled with 36 mg/ml nicotine, 50%/50% (w/v) PG/VG, non-flavored e-liquid (American E-liquid) was vaped using an automated vaping robot programmed with experienced e-cigarette user patterns (i.e. puff volume: 70 ml, duration: 3s, frequency: 20s) and resulting vapor was extracted via a liquid impinger. 1 uM of pure (-)-nicotine liquid (Sigma Aldrich) was used as a positive control. Total miRNA was collected with the mirVana miRNA isolation kit. miRNA concentration and quality was measured by spectrophotometry and expression was analyzed with Affymetrix GeneChip miRNA 4.0 Arrays. Results were normalized against human-positive and negative chip controls using Robust Multi-Array Average Normalization.

2019-09-30 | E-MTAB-7893 | 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