Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA profiling of human prostate cancer cell lines treated with 5azadC and TSA to investigate epigenetic modifications

ABSTRACT: miRNA expression profiling of prostate cancer cell lines, PC-3, DU145, LAPC-4, VCaP, LNCaP, 22rv1, and normal prostate epithelial cells, PrECs, was done after treating the cells with DNA demethylating agent 5-aza-2'-deoxycytidine (5azadC; Sigma-Aldrich, St. Louis, MO) and histone deacetylase inhibitor trichostatin A (TSA; Sigma-Aldrich). These treatments relieve epigenetic modifications, and thus reveal potentially epigenetically silenced miRNAs amongst the miRNAs with increased expression after the treatments.

ORGANISM(S): Homo sapiens

DISEASE(S): prostate carcinoma

SUBMITTER: Hanna Rauhala

PROVIDER: E-MEXP-2313 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

miR-193b is an epigenetically regulated putative tumor suppressor in prostate cancer.

Rauhala Hanna E HE Jalava Sanni E SE Isotalo Jarkko J Bracken Hazel H Lehmusvaara Saara S Tammela Teuvo L J TL Oja Hannu H Visakorpi Tapio T

International journal of cancer 20100901 6

miRNAs have proven to be key regulators of gene expression and are differentially expressed in various diseases, including cancer. Our aim was to identify epigenetically dysregulated genes in prostate cancer. We performed miRNA expression profiling after relieving epigenetic modifications in 6 prostate cancer cell lines and nonmalignant prostate epithelial cells. Thirty-eight miRNAs showed increased expression in any prostate cancer cell line after 5-aza-2'-deoxycytidine (5azadC) and trichostati ...[more]

PMID: 20073067

Similar Datasets

Transcription profiling of mouse prostate cancer TRAMP-C2 treated with demethylating agent 5-aza-2-deoxycytidine vs untreated to identify silenced transcripts

Project description:Gene expression profiling of TRAMP-C2, transgenic adenocarcinoma of mouse prostate, cell line was done after treating the cells with DNA demethylating agent 5-aza-2'-deoxycytidine (5azadC; Sigma-Aldrich, St. Louis, MO) and histone deacetylase inhibitor trichostatin A (TSA; Sigma-Aldrich), both separately and in combination. These treatments relieve epigenetic modifications, and thus reveal potentially epigenetically silenced genes amongst the genes with increased expression after the treatments.

2008-09-12 | E-MEXP-1611 | biostudies-arrayexpress

Transcription profiling by array of human bladder cancer cell lines with or without TP53 mutations

Project description:The established cell lines RT4, 5637 and T24 from human bladder TCC were obtained from the Cell Bank of the Federal University of Rio de Janeiro, Brazil. The 5637 cells harbor two TP53 mutations, at codon 72 (Arg . Pro) and codon 280 (Arg . Thr).T24 cells contain a TP53 allele encoding an in-frame deletion of tyrosine 126. Both cell lines were established from high-grade bladder tumors. No specific mutations were detected in RT4 cells, which had been established from a low-grade papillary bladder tumor. The RT4 and T24 cell lines were maintained in DulbeccoM-^Rs modified EagleM-^Rs medium (Sigma-Aldrich, Inc, St Louis, MO, USA), and the 5637 cells were kept in Roswell Park Memorial Institute medium (Sigma-Aldrich). Both media were supplemented with 10% fetal bovine serum (Cultilab Ltd, Campinas, Brazil), 100 U/mL penicillin G (Sigma-Aldrich), 100 U/mL streptomycin (Sigma-Aldrich) and 1% kanamycin sulfate (Amresco, Branded Products Group, Solon, OH, USA); cells were cultured at 37M-:C in an atmosphere of 5% CO2. A pooled reference design was chosen. More specifically, each array was hybridized with the same reference sample labeled with Cy5, while the experimental samples (control or treated) were labeled with Cy3.

2010-10-30 | E-MEXP-2859 | biostudies-arrayexpress

The RNA-binding protein HuR coordinates global changes in gene expression during patterning of early peripheral nerves

Project description:Identify mRNA targets of the RNA-binding protein HuR in vivo during Schwann cell development using RIP-chip analysis. IP protocol of endogenous mRNA-transfected HuR complexes was performed as described in Keene et al. (2006). In brief, 500 mg of whole-cell lysate obtained from a pool of NB or P5 sciatic nerves from C57BL6J mice were incubated with a suspension of Protein Sepharose beads (Sigma-Aldrich), pre-coated with 15 mg of either IgG1 (BD Pharmingen) or anti-HuR (Santa Cruz Biotechnology) antibodies. mRNAs were isolated using the phenol-chloroform method.

2012-01-19 | E-MEXP-3519 | biostudies-arrayexpress

LHK2 SP

Project description:We used the commercially available amino-allyl RNA amplification Kit ver,2 (High Yield Type) (SIGMA-ALDRICH). Purified total RNA (3 ?g) was reverse-transcribed to generate double-stranded cDNA using an oligo dT T7 promoter primer and reverse transcriptase. Next, cRNA was synthesized using T7 RNA polymerase, which simultaneously incorporated Cy3- or Cy5-labeled cytidine triphosphate. During this process, the samples of SP cells were labeled with Cy5, whereas the non-SP cells were labeled with Cy3 as control cells. Quality of the cRNA was again checked using the Nano Drop. Cy3-labeled cRNA and Cy5-labeled cRNA were combined and then fragmented in a hybridization cocktail (SIGMA-ALDRICH). Then the labeled cRNAs were hybridized to a 60-mer probe oligonucleotide microarray and incubated for 20 h ours at 50 ?C. The fluorescent intensities were determined by a Genepix 4000B Microarray Scanner (Axon, US).

2014-05-02 | E-MEXP-3913 | biostudies-arrayexpress

MicroRNA profiling of human prostate cancer

Project description:miRNA expression profiling of 13 clinical prostate samples, 4 benign prostate hyperplasias, 5 untreated primary prostate carcinomas and 4 castration-resistant prostate cancers.

2010-01-31 | E-MEXP-2319 | biostudies-arrayexpress

curcumin aorta apoEKO mice

Project description:At eight weeks of age, male mice were divided into two groups (15 mice per group) fed iso-energetic diet: a control-diet or the same diet supplemented with 0.2% of curcumin (Sigma Aldrich) for 16 weeks (Table S1). The dose of curcumin used in this study is equivalent to 1g curcumin consumption in humans, a level of consumption achievable in South-Asian countries. No significant difference in weight gain was observed between the two groups at the end of the experimental period (data not shown). After 16 weeks, mice were anaesthetized (40 mg pentobarbital/kg of body weight) and blood was collected from the abdominal aorta into heparinised tubes and plasma was stored at -80 C. After washing with sterilized PBS, aorta and heart samples were immediately frozen in liquid nitrogen and stored at -80 C. Original processed data are available in the archive: http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-3185/E-MEXP-3185.additional.zip

2012-04-15 | E-MEXP-3185 | biostudies-arrayexpress

Expression Profiles of HepG2 cells treated with following compounds: Azathriopine, Furan, Tetradecanoyl phorbol acetate, Tetrachloroethylene, Diazinon and Dmannitol

Project description:The transcriptomic changes induced in the human liver cell line HepG2 by Azathriopine (250µM, Sigma-Aldrich), Furan (2mM, Sigma-Aldrich), Tetradecanoyl phorbol acetate (500nM, Sigma-Aldrich), Tetrachloroethylene (2mM, Sigma-Aldrich), Diazinon (250µM, Sigma-Aldrich) and Dmannitol (250µM, Sigma-Aldrich) during 4, 8, 24, 48 and 72hrs As a solvent control for Azathriopine, Furan, Diazinon and Tetradecanoyl phorbol acetate, DMSO was used (0.5%); As a solvent control for tetrachloroethylene, ethanol was used (0.5%); As a solvent control for D-mannitol, HBSS was used (0.5%)

2015-01-13 | GSE58235 | GEO

Transcriptional Profile of Perinatal Rat Pancreas

Project description:Pancreata were excised from offspring of time-mated Wistar rats age 10-11 weeks (Taconic, Lille Skensved, Denmark) at embryonic day 20 (E20), immediately after birth (P0) and two days after birth (P2). After decapitation, individual pancreata were quickly dissected and placed directly in ice cold TRIReagent (Sigma-Aldrich, St Louis, MO, USA). RNA from individual pancreata was kept separately in order to verify the array results in pools of RNA as well as in individual animals by real time qPCR. 0.5 M-5g of RNA from each of 3 male and 3 female littermates were pooled at each time-point (E20, P0 and P2). This was repeated in each of three biological independent replicate experiments giving a total of 9 pooled samples, three at each time points

2012-02-01 | E-MEXP-3174 | biostudies-arrayexpress

MicroRNA profiling of human precursor B-cell acute lymphoblastic leukemia cell line NALM-6 after trichostatin A treatment

Project description:Expression profile of miRNAs in NALM-6 cells were analyzed after TSA treatment for 6h, compared with non-treated cells.

2009-11-06 | E-MEXP-2047 | biostudies-arrayexpress

Transcription profiling of human gastric cancer cells after treatment with 5-aza-2-deoxycytidine and 4-phenylbutyric acid

Project description:Gene expression profiling in human gastric cancer cells after 5-aza-2'-deoxycytidine (5-Aza-CdR) and 4-phenylbutyric acid (PBA) treatment was analyzed to investigate what genes are controlled by these chromatin modifying drug

2008-10-09 | E-MEXP-1821 | 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