Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of lung adenocarcinoma cell line Wnt responsive signature

ABSTRACT: Identify Wnt3A responsive signature in lung adenocarcinoma cells Experiment Overall Design: 4 different cell lines +/- Wnt3A; replicate samples

ORGANISM(S): Homo sapiens

SUBMITTER: Nguyen Don

PROVIDER: S-ECPF-GEOD-14107 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Lung adenocarcinoma cell line Wnt responsive signature

Project description:Identify Wnt3A responsive signature in lung adenocarcinoma cells

2009-07-10 | GSE14107 | GEO

Transcription profiling of lung adenocarcinoma cell line Wnt responsive signature

Project description:Identify Wnt3A responsive signature in lung adenocarcinoma cells Experiment Overall Design: 4 different cell lines +/- Wnt3A; replicate samples

2009-07-19 | E-GEOD-14107 | biostudies-arrayexpress

Transcription profiling of human lung adenocarcinoma derived cell line A549 treated with testosterone

Project description:Effect of testosterone treatment on gene expression of lung adenocarcinoma derived cell line A549

| S-ECPF-MEXP-2003 | biostudies-other

Transcription profiling of human lung adenocarcinoma derived cell line A549 treated with dexamethasone

Project description:Effect of dexamethasone on gene expression in lung adenocarcinoma derived cell line A549

| S-ECPF-MEXP-2004 | biostudies-other

Transcription profiling of human A549 lung adenocarcinoma cell line time Course of TGF-beta treatment

Project description:Time Course of TGF-beta treatment of A549 lung adenocarcinoma cell line on Affymetrix HG_U133_plus_2 arrays; triplicate experiments. The goal of the experiment is to profile temporal gene expression changes during TGF-beta-induced epithelial-mesenchymal transition (EMT). During EMT cancer cells loose their epithelial specifc proteins and gain mesenchymal proteins to acquire migratory and invasive phenotype essential for metastasis. Human A549 lung adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 0, 0.5, 1, 2, 4, 8, 16, 24, and 72 h to induce EMT. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques. We provide the raw .CEL files and a supplementary Excel spreadsheet with log-transformed data and selected results from a statistical analysis. Experiment Overall Design: Human A549 lung adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 0, 0.5, 1, 2, 4, 8, 16, 24, and 72 h. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques. The 2 h sample of the third experiment was not run on an array due to poor RNA, so that only 26 arrays were run.

| S-ECPF-GEOD-17708 | biostudies-other

Transcription profiling of human GRE specific DNA-binding polyamide effect on dexamethasone-stimulated lung adenocarcinoma cell line

Project description:Analysis of dexamethasone-stimulated A549 lung adenocarcinoma epithelial cells treated with a glucocorticoid response (GR) element (GRE) specific DNA binding polyamide. Polyamide designed to target the sequence 5'-WGWWCW-3' and disrupt GR-mediated gene expression. Effects of the GR antagonist mifepristone also examined. Experiment Overall Design: A549 cells were treated with compounds for 48 hours before RNA extraction and hybridization on Affymetrix microarrays.

| S-ECPF-GEOD-17307 | biostudies-other

Transcription profiling of human non-small cell lung cancer adenocarcinoma and squamous cell carcinoma subtypes

Project description:Non-small cell lung cancer (NSCLC) can be classified into the major subtypes adenocarcinoma (AC) and squamous cell carcinoma (SCC) subtypes. Although explicit molecular, histological and clinical characteristics have been reported for both subtypes, no specific therapy exists so far. However, the characterization of suitable molecular targets holds great promises to develop novel therapies in NSCLC. In the present study, global gene expression profiling of 58 human high grade NSCLC specimens revealed large transcriptomic differences between AC and SCC subtypes: More than 1.700 genes were found to be differentially expressed. Experiment Overall Design: The NSCLC patient collective was composed of the histological subtype adenocarcinoma (n=40) and squamous cell carcinoma (n=18). We subjected gene expression profiles of 40 AC and 18 SCC samples into further analysis. Unsupervised hierarchical clustering of all 58 NSCLC tumors using the 500 most variably expressed transcripts revealed two different clusters, which were strongly associated with the histological subtypes AC and SCC of NSCLC. Our result indicated that the major impact on global transcriptional changes was due to the NSCLC histology.

| S-ECPF-GEOD-10245 | biostudies-other

Transcription profiling of human stage non-small cell lung cancer samples, metaanalysis for a predictive signature

Project description:We applied a meta-analysis of datasets from seven different microarray studies on lung cancer for differentially expressed genes related to survival time (under 2 y and over 5 y). Systematic bias adjustment in the datasets was performed by distance-weighted discrimination (DWD). We identified a gene expression signature consisting of 64 genes that is highly predictive of which stage I lung cancer patients may benefit from more aggressive therapy. Experiment Overall Design: RNA was extracted from frozen tissue of primary stage I Non-Small Cell lung tumors for gene array analysis

| S-ECPF-GEOD-6253 | biostudies-other

Systematic profiling of invasion-related gene signature predicts prognostic features of lung adenocarcinoma.

Project description:Due to the high heterogeneity of lung adenocarcinoma (LUAD), molecular subtype based on gene expression profiles is of great significance for diagnosis and prognosis prediction in patients with LUAD. Invasion-related genes were obtained from the CancerSEA database, and LUAD expression profiles were downloaded from The Cancer Genome Atlas. The ConsensusClusterPlus was used to obtain molecular subtypes based on invasion-related genes. The limma software package was used to identify differentially expressed genes (DEGs). A multi-gene risk model was constructed by Lasso-Cox analysis. A nomogram was also constructed based on risk scores and meaningful clinical features. 3 subtypes (C1, C2 and C3) based on the expression of 97 invasion-related genes were obtained. C3 had the worst prognosis. A total of 669 DEGs were identified among the subtypes. Pathway enrichment analysis results showed that the DEGs were mainly enriched in the cell cycle, DNA replication, the p53 signalling pathway and other tumour-related pathways. A 5-gene signature (KRT6A, MELTF, IRX5, MS4A1 and CRTAC1) was identified by using Lasso-Cox analysis. The training, validation and external independent cohorts proved that the model was robust and had better prediction ability than other lung cancer models. The gene expression results showed that the expression levels of MS4A1 and KRT6A in tumour tissues were higher than in normal tissues, while CRTAC1 expression in tumour tissues was lower than in normal tissues. The 5-gene signature prognostic stratification system based on invasion-related genes could be used to assess prognostic risk in patients with LUAD.

| S-EPMC8256358 | biostudies-literature

Identification of Wnt responsive genes using a murine mammary epithelial cell line model system.

Project description:The Wnt/Wg pathway plays an important role in the developmental program of many cells and tissues in a variety of organisms. In addition, many Wnts and components of their downstream signaling pathways, such as beta-catenin and APC, have been implicated in tumorigenesis. Over the past years, several genes have been identified as Wnt responsive, including c-myc, siamois, and cyclin D1.In order to identify additional genes responsive to Wnt signaling that contribute to the transformed phenotype, we performed a cDNA subtractive hybridization screen between a mouse mammary epithelial cell line that overexpresses Wnt-1 (C57MG/Wnt-1) and the parental cell line (C57MG). The screen identified a total of 67 genes to be up-regulated in response to Wnt signaling. Of these 67 genes, the up-regulation of 62 was subsequently confirmed by Northern and dot blot analyses (and, for a subset, semi-quantitative PCR) of RNA isolated from C57MG cells subjected to (1) an independent Wnt-1 retroviral infection, and (2) co-culture with Wnt-1 expressing cells. Among the confirmed Wnt-1 responsive genes, we further characterized a mouse homolog of the human transcription factor Basic Transcription Element Binding protein 2 (BTEB2), Wnt-1 Responsive Cdc42 homolog (Wrch-1), and Wnt-1 Induced Secreted Protein (WISP-1).Several novel genes were identified in this screen, as well as others that have been shown previously to be regulated by Wnt signaling, such as connexin43. The results indicate that cDNA subtractive hybridization is a useful method for identifying genes involved in the process of Wnt-1-induced transformation.

| S-EPMC425575 | biostudies-literature

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