Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Gene Regulation Pattern from Lung Cancer Human Tissues

ABSTRACT: To identify individual genes with potential diagnostic and therapeutic utilities in lung cancer, we performed gene expression profiling out of a broad coverage of human transcriptome using clinical patient tissues. Six RNA samples extracted from five cancerous tissues and one normal control were subjected to Affymetrix gene array analysis using Human Exon 1.0 ST Array. Data were further processed using Expression Console and Transcriptome Analysis Console softwares. Both core-gene expression analysis and extended-gene expression analysis were performed to discover significantly regulated genes associated with lung cancer progression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE63571 | GEO | 2014/11/30

SECONDARY ACCESSION(S): PRJNA268680

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GeneChip Expression Array

Project description:Gene expression analysis to compare control cells and sorted cells We transfected cDNA of human umbilical vein endothelial cells into rat myeloma cells, and sorted cells bound to patient IgG. Sorted cells were analyzed using the Affymetrix Human Genome U133 Plus 2.0 Array to investigate the cDNA inserted into the sorted cells. Array data was processed by Affymetrix GeneChip Command Console Software and Affymetrix Expression Console Software. No techinical replicates were performed.

2020-02-17 | GSE145367 | GEO

Transcription profiling of liver, pancreas and lung tissue of male SD rats and CRISPR/Cas-9-mediated knockout SD-Nme7-/- male rats

Project description:We aimed to compare the transcriptome of liver, pancreas, and lung tissue of adult male SD rats and the novel CRISPR/Cas-9-mediated knockout SD-Nme7-/- adult male rats using Affymetrix Rat Gene 2.1 ST Array Strip. Total RNA was isolated from the liver, pancreas, and lung tissues (RNeasy Mini Kit, Qiagen) of SD and SDNme7-/- rats. The quality and integrity of the total RNA was evaluated on the Agilent 2100 Bioanalyzer system (Agilent, Palo Alto, CA). Microarray experiments were performed using the Rat Gene 2.1 ST Array Strip. The whole hybridization procedure was performed using the Affymetrix GeneAtlas® system according to the manufacturer's instructions. The quality control of the chips was performed using Affymetrix Expression Console. After applying quality filters and data normalization by the Robust Multichip Average (RMA) algorithm implemented in Affymetrix Expression Console, the set of obtained differentially expressed probesets was filtered by the false discovery rate (FDR) method implemented in PARTEK Genomics Suite 7 (Partek, St. Louis, Missouri). Transcriptomic data were then processed by a standardized sequence of analyses (hierarchical clustering and principal component analysis, gene ontology, gene set enrichment, Upstream Regulator Analysis, Mechanistic Networks, Causal Network Analysis, and Downstream Effects Analysis) using Ingenuity Pathway Analysis.

2021-04-06 | E-MTAB-10000 | biostudies-arrayexpress

Transcriptome expression study for miRNA-mRNA target discovery

Project description:Total RNA was collected from DU145-control(scr) and DU145-miR-106a transfected cells. Gene expression analysis was performed by The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) using Affymetrix GeneChip Human Gene 2.0 ST array. Data were normalized using the default parameters in Affymetrix Expression Console Software 1.4. Genes downregulated 0.8-fold in miR-106a compared to control(scr) were identified as possible mRNA targets.

2018-12-03 | GSE107046 | GEO

Comparing transcrional changes in Plasmodium yoelii infected to uninfected primary hepatocytes

Project description:GFP expressing Plasmodium yoelii (Py-GFP) infected, or naïve cultured primary hepatocytes were FACS sorted and re-suspended in TRIzol and RNA purified with RNAeasy kit (Qiagen).RNA was assessed for purity and quality using an Agilent 2100 Bioanalyzer and transcriptome analysis performed on Affymetrix GeneChip Mouse Transcriptome array 1.0. Data output was analyzed and visualized using Affymetrix Expression Console 4.0.

2021-10-18 | GSE186023 | GEO

Comparing transcrional changes in Plasmodium yoelii infected to uninfected primary hepatocytes

2019-05-10 | GSE130961 | GEO

Expression data of miRNA profile from colorectal cancer and the adjacent normal tissues infected with F. nucleatum

Project description:Expression data of miRNA profile from colorectal cancer and the adjacent normal tissues infected with F. nucleatum. Colorectal cancer(CRC) is among the most common cancer types in the world and one of the most lethal cancers. Fusobacterium nucleatum (F. nucleatum) plays an etiologic role in the development of colorectal cancer, but specific tumor molecules involved in the progression of CRC induced by F. nucleatum is not clear. This study investigated some miRNAs and the genes involved in the progression of F. nucleatum-induced colorectal cancer by Affymetrix miRNA microarray technology. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes between Colorectal cancer and the adjacent normal tissues (CONTROL) infected without F. nucleatum . The miRNA array was performed using the affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, California, United States). The chip was processed using a commercial Affymetrix array service (GeneTech Biotechnology Limited Company, Shanghai, China). The affymetrix GeneChip® miRNA 3.0 Array contains 2,999 probe sets unique to human, mouse and rat pre-miRNA hairpin sequences, 2,216 human snoRNA and scaRNA probe sets and covers 153 organisms (19,724 probe sets). Raw data sets were extracted from all Cel files (raw intensity file) after scanning of slides. These raw data sets were separately analyzed using Expression Console and GeneSpring GX12.5 software followed by differential miRNA expression, fold change & cluster analysis.

2018-11-06 | GSE122182 | GEO

Expression profile of bone marrow HSCs from healthy donors

Project description:mRNA samples from bone marrow CD34+ cells (HSC) from healthy donors after co-culture assays (Control condition, with hMSCs and CD34+ cells from healthy donors; and AML condition, with hMSCs-AML and CD34+ cells from donors) were amplified, labeled and hybridized to the ClariomTM S Array human (Thermo Scientific, USA). Normalization and analysis of microarray data was performed using the Transcriptome Analysis Console (TAC) software (Affymetrix, USA).

2024-04-26 | GSE253556 | GEO

Microarray-analysis of primary lung fibroblasts cell lines (established from 3-4weeks old mice)

Project description:Purpose: The goal of this analysis is to compare gene expression profiling of activated-fibroblasts lines (expressing K-RasG12D) to non-activated-fibroblast expressing WT K-Ras. Methods: Fibroblasts lines were obtained after lung-tissue digestion with collagenase. Cells were homogenized in TRIzol reagent and total RNA was extracted according to manufacturer’s protocol. Hybridization of RNA was performed using Affymetrix Mouse-Gene 1.0ST platform by Dana Farber Microarray Core Facility and data analysis was performed using dChip software. Gene expression analysis was conducted using Transcriptome Analysis Console Software (TAC) using comparing method (SKY vs WT). Results: Gene expression analysis revealed deregulation of several canonical genes involved in different signaling pathways, as Wnt, Notch and Hedgehog signaling pathways. Deregulations of ECM remodeling and focal adhesion expression were reported as well. In addition the secreted molecule Hgf was increased in activated fibroblasts compared to WT line.

2024-02-12 | GSE166781 | GEO

Gene expression profiling of AGS Gastric Cancer cells upon YY1 knock down

Project description:Yin Yang 1 (YY1) is a ubiquitous transcription factor belonging to the GLI-Kruppel class of zinc finger proteins regulating diverse biological processes including cell proliferation, development, DNA damage responses and also involved in carcinogenesis. The protein is involved in repressing and activating a diverse number of promoters.In order to study the role of the transcription factor YY1 in gastric cancer, transcriptome wide gene expression analysis was performed upon silencing the YY1 gene in gastric cancer cell line, AGS using Affymetrix Human Transcriptome 2.0 array. Transcriptome Analysis Console (TAC) Software was used for the analysis of differentially expressed genes between AGS_YY1_siRNA transfected and AGS_NTC_siRNA transfected cells.

2021-03-31 | GSE163164 | GEO

Expression data from primary tissue, human oral mucosa (mRNA data)

Project description:The experiment aims to identify regulatory miRNA networks influencing mRNA profiles in oral lichen planus (OLP). RNA and miRNA were extracted simultaniously using miRVana (Ambion, Life Technologies). Sample and array processing was carried out according to the manufacturer's guidelines. Affymetrix raw data was processed using AGCC Expression Console 1.1 (Affymetrix), employing RMA normalization. Linking miRNA and mRNA was performed with a correlation analysis, while a false discovery rate was used to exclude false-positive correlations between miRNAs and their predicted targets.

2013-05-06 | GSE38616 | GEO

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