Name: RNA-seq of coding RNA from human IMR-32 cells treated with azakenpaullone, BIO or LiCl to investigate GSK-inhibitor treatment
Keywords: RNA-seq of coding RNA

Home
Browse
Submit Data
API
Database
Help
Login

Dataset Information

141 Views

41 Connections

2 Citations

0 Reanalyses

2 Downloads

Omics score: 112

RNA-seq of coding RNA from human IMR-32 cells treated with azakenpaullone, BIO or LiCl to investigate GSK-inhibitor treatment

ABSTRACT: Cells were cultured in RPMI 1640 (Gibco), supplemented with 10% fetal bovine serum (FBS) (Gibco), 2mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin solution (Gibco). IMR32 cells were treated as follows; untreated control, 24h 1uM azakenpaullone, 24h 1uM BIO or 24h 28mM LiCl with biological duplicates.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Homo sapiens

SUBMITTER: David J Duffy Thomas Schwarzl

PROVIDER: E-MTAB-1684 | ArrayExpress | 2015-01-08

SECONDARY ACCESSION(S): ERP003495

REPOSITORIES: ArrayExpress, ENA

ACCESS DATA

Json Xml

Publications

Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma.

Duffy David J DJ Krstic Aleksandar A Halasz Melinda M Schwarzl Thomas T Fey Dirk D Iljin Kristiina K Mehta Jai Prakash JP Killick Kate K Whilde Jenny J Turriziani Benedetta B Haapa-Paananen Saija S Fey Vidal V Fischer Matthias M Westermann Frank F Henrich Kai-Oliver KO Bannert Steffen S Higgins Desmond G DG Kolch Walter W

Oncotarget 20151201 41

Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-drugga ...[more]

PMID: 26673823

Similar Datasets

Retinoic acid and Azakenpoullone treatment in SH-SY5Y/6TR(EU)/pTrex-Dest-30/MYCN cell line in high and low MYCN levels

Project description:The effect of the GSK3 inhibitor Azakenpaullone (Azak) and the differentiation agent retinoic acid (RA) was studied in low and high MYCN levels in the MYCN inducible neuroblastoma cell line SH-SY5Y/6TR(EU)/pTrex-Dest-30/MYCN (SY5Y-MYCN). Azak was dissolved in DMSO in order to apply it to the cells. Therefore a vehicle control consisting of SY5Y-MYCN cells treated with 24h 1 ul/ml DMSO only was used in duplicates. Doxycycline (Sigma) dissolved in water was used at a final concentration of 1ug/ml to induce MYCN expression in SY5Y-MYCN. A co-treatment study with Dox and Azak was conducted. SY5Y-MYCN cells were treated with 24h Azak, 24h Azak & 48h Dox and 48h Dox, with biological duplicates. 1 uM RA (dissolved in DMSO) and 1 ug/mL Doxycycline were given individually and in combination. SY5Y-MYCN cells were treated with 24h RA, 24h RA & 48h Dox, and 48h Dox and RNA was extracted in biological duplicates. For the 24h RA & 48h Dox co-treatment cells were treated with Dox for 24h and then with RA and fresh Dox for a further 24h.

2014-12-11 | E-MTAB-2689 | ArrayExpress

Timecourse total transcriptome sequencing of MCF10A cells undergoing acinus formation.

Project description:RNA-seq was performed for transcriptional analysis of MCF10A cells, an epithelial mammary cell line. MCF10A cells were cultured in 3D acinus forming conditions (in Matrigel). Timepoints analysed were 24h, 34h, 36h, 38h and 48h into acinus formation. Control cells were monoloayer.

2014-09-26 | E-MTAB-2969 | ArrayExpress

RNA-seq of MYCN overexpression in SH-SY5Y/6TR(EU)/pTrex-Dest-30/MYCN cell line

Project description:MYCN overexpression in the doxycline MYCN inducible cell line SH-SY5Y/6TR(EU)/pTrex-Dest-30/MYCN (SY5Y-MYCN) using the dynamic transcriptome analysis (DTA) protocol. Samples at different time-points after MYCN over-expression and uninduced controls (0h) were sequenced in duplicates. The experimental setup consists of [A] total mRNA at 0h, 1h, 4h, 24h, which corresponds to the standard mRNA-seq protocol, [B] 4-thioUridine (4sU) labelled mRNA 30 min before extraction at time-points 0h, 1h, 4h, which is the freshly transcribed mRNA within the last 30 min before the time-point and [C] the counter-part, 4sU unlabelled mRNA 30 min before extraction which corresponds to the mRNA from before 30 min of extraction. The samples were sequenced on an Illumina GA IIx using the Illumina protocols.

2017-01-30 | E-MTAB-2691 | ArrayExpress

RNA-seq of human neuroblastoma cell lines

Project description:Untreated neuroblastoma cell lines SMS-KCN, SMS-KCNR, Kelly, and SH-SY5Y were sequenced on an Illumina GA IIx sequencer.

2017-01-30 | E-MTAB-2690 | ArrayExpress

Genomic Redistribution of GR Monomers and Dimers Mediates the Transcriptional Response to Exogenous Glucocorticoid In Vivo.

Project description:Expression profiles of GRdim mutant macrophages (mouse, bone-marrow derived) treated with LPS for 6 hrs or with LPS (6hrs) + Dex (O/N 1uM). Identification of GR-regulated genes in response to LPS. 3 Grdim mutant macrophages samples treated with LPS (6hrs) and 3 Grdim mutant macrophage samples treated with LPS (6hrs) and Dex (overnight).

2015-04-30 | E-GEOD-68160 | ArrayExpress

MYCN regulated miRNAs

Project description:miRNAs which are differentially expressed upon MYCN overexpression (1h, 4h and 24h after induction) in a neuroblastoma line were detected using deep sequencing.

2014-07-24 | E-MTAB-2787 | ArrayExpress

Global gene profiling of (-)-Epigallocatechin-3-gallate (EGCG)-induced neuronal death

Project description:Alzheimer’s disease (AD) is the most common form of adult-onset dementia with severe intellectual deterioration and is characterised by the accumulation of the amyloid-β (Aβ) peptides and the presence of hyperphosphorylated microtubule- associated protein, tau. (-)-Epigallocatechin-3-gallate (EGCG) – a polyphenolic catechin found in green tea leaves, not only acts as a proteasome inhibitor, it is also involved in neuroprotection. A total of 7 RNA samples were analyzed. Cultured murine primary cortical neurons were treated with 1uM EGCG for 24h (n=3) in addition to the vehicle control (n=4).

2014-06-02 | E-GEOD-22996 | ArrayExpress

A gene expression signature of PDGF-stimulated fibroblasts

Project description:Analysis of platelet-derived growth factor (PDGF)-stimulated fibroblasts. Results provide insight into novel pro-tumorigenic factors induced by PDGF-activation of fibroblasts. 1.2 x 10e6 BJ-hTERT fibroblasts were cultured in 10cm dish with Dulbecco's Modified Eagle Medium (DMEM; Gibco Life Technologies, Gergy-Pontoise, France) containing 1% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, penicillin (100 units/ml) and streptomycin (100 ng/ml) at 37ºC in a 5% CO2 humidified atmosphere during 24h. Cultures were stimulated with or without 20ng/mL PDGF-BB (Peprotech, New Jersey, USA) for another 24h prior to harvest. Unstimulated fibroblasts were used as control samples. Cultures of both unstimulated and stimulated fibroblasts were done in triplicate.

2012-09-26 | E-GEOD-40720 | ArrayExpress

Next generation sequencing profiling identifies miR-574-3p and miR-660-5p as potential novel prognostic markers for breast cancer

Project description:Prognostication of Breast Cancer (BC) relies largely on traditional markers such as hormone or growth factors but due to their suboptimal specificities, it is challenging to identify the subset of patients who are likely to undergo recurrence and markers of higher specificity are sought to guide therapies. MicroRNAs (miRNAs) are small non-coding RNAs which function as post-transcriptional regulators of gene expression and have shown promise as potential prognostic markers in several cancer types including BC. In our study, we sequenced 104 breast tumor tissue samples and 11 apparently healthy normal breast tissues for miRNAs. Two widely used approaches were adopted to identify prognostic markers – Case-control and Case-only. For both the approaches, Cox-proportional hazards regression model and risk score analysis was performed to identify miRNA signature independent of potential confounders. Representative miRNAs were validated using qRT-PCR. Gene ontology terms were identified for miRNAs significant in survival analysis. A total of 1,423 miRNAs were captured from the tissues, of which 126 were retained with predetermined criteria for good read counts. In the case-control approach, 80 miRNAs were differentially expressed, from which four and two miRNAs were significant for OS and RFS respectively. In the case-only approach, from 147 miRNAs, 11 and four miRNAs were significant for OS and RFS respectively, in which miR-574-3p and miR-660-5p were novel and were not previously found to be associated with BC prognosis. Multivariate Cox analysis indicated that the risk scores calculated in both the approaches were potential independent prognostic factors for BC. Targets for the identified miRNAs were enriched for cell proliferation, invasion and migration. Identification of miRNAs as prognostic markers for breast cancer

2016-03-17 | E-GEOD-68085 | ArrayExpress

HCT116 cells treated with the p97 inhibitior CB-5083

Project description:The goal of this study was to analyze differential gene expression 8 hr after treatment of CB-5083, a small molecule inhibitor of p97 (VCP), in HCT116 cells grown in culture. DMSO treated cells were compared to cells treated with 1uM CB-5083 after 8 hr.

2015-12-01 | E-GEOD-73588 | ArrayExpress

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
GPMDB

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS

ArrayExpress
ExpressionAtlas

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data