Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

133 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression analysis of Human pancreatic cancer cell line Panc1 pretreated with DMSO and Clofibrate.

ABSTRACT: Investigation of whole genome gene expression level changes of Panc1 pretreated with Clofibrate, compared to Panc1 pretreated with DMSO. Compare differentially expressed genes by analyzing mRNA profilings between DMSO and Clofibrate pretreating Panc1 cell.

ORGANISM(S): Homo sapiens

SUBMITTER: Shuyu Zhang

PROVIDER: E-GEOD-69650 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Analysis of wheat straw grown Trichoderma reesei gene expression as influenced by L-methionine in the medium

Project description:Wheat straw grown cultures of T. reesei QM9414 were supplemented with 100 µM L-methionine and the genome wide gene expression monitored in order to find novel L-Methionine repressible genes. Total RNA was isolated from independent duplicate shake flask cultures of T. reesei QM9414 pregrown on pretreated wheat straw. Global gene and analyzed using a 4 chip design where 2 chips each represented cultures with or without exogeneously added 100 µM L- Methionine.

2015-06-11 | E-GEOD-69745 | biostudies-arrayexpress

Expression analysis of RNAi mediated ALPPL2 knockdown in ALPPL2 expressing Panc-1 cells (Panc-1+ve)

Project description:Analysis of differentially expressing genes in whole genome wide analysis of ALPPL2 expressing Panc-1 cells (Panc-1+ve) via siRNA mediated knockdown of ALPPL2 Panc-1 +ve and Panc-1-ve cell lines were generated from Panc-1 cell line based upon its hetergenous binding to aptamer SQ2. Detailed procedure of generation of these cell lines are described in Pooja Dua, Hye Suk Kang, Seung-Mo Hong, Ming-Sound Tsao, Soyoun Kim, and Dong-ki Lee. 2012 Alkaline Phosphatase ALPPL2 is a novel pancreatic carcinoma-associated protein. Cancer Research A four chip study using total RNA recovered from Panc-1+ve cells transfected with siALPPL2-2, siALPPL2-3, siGFP control and Lipofectamine 2000 treatament . Each chip measures 45,033 genes with three 60 mer probe pairs per target.

2012-11-21 | E-GEOD-42427 | biostudies-arrayexpress

Alkaline Phosphatase ALPPL2 is a novel pancreatic carcinoma-associated protein

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-11-21 | E-GEOD-42429 | biostudies-arrayexpress

Expression analysis of Human pancreatic cancer cell line Panc1 pretreated with DMSO and Clofibrate.

Project description:Investigation of whole genome gene expression level changes of Panc1 pretreated with Clofibrate, compared to Panc1 pretreated with DMSO.

2015-06-09 | GSE69650 | GEO

The gene expression profiling array of LncRNA between tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma

Project description:Investigation of whole genome gene expression level changes of LncRNAs in tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma. The different expression genes were further analysised. The human LncRNA microarray analysis of the 10 samples (5 non-tumor tissues and 5 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples.

2013-08-10 | E-GEOD-49713 | biostudies-arrayexpress

Identification of the genetic loci associating with the OMV formation by means of transcriptome analysis on the isogenic BF2766 mutants in B. fragilis strain YCH46

Project description:The human gut microbe Bacteroides fragilis can alter the expression of its surface molecules such as capsular polysaccharides and SusC/SusD family outer membrane proteins through the reversible DNA inversions.ã??We have revealed that the outer membrane vesicle (OMV) formation in B. fragilis is regulated by BF2766 (tyrosine recombinase)-mediated DNA inversions at two distantly located promoter regions previously designated as class IV regions. In this study, we aimed to identify the genetic loci associating with the OMV formation by means of transcriptome analysis on the isogenic BF2766 mutants. By comparing the transciptomes of four BF2766 deletion mutants, in which the promoter orientations in class IV-1 and IV-2 regions were locked ON/ON, OFF/ON, OFF/OFF, or ON/OFF, we found that the transcription of the genes downstream of class IV-2 markedly elevated in a hyper-vesiculating ON/ON strain. A four chip study using total RNA isolated from four BF2766 deletion mutants culture. Each sample contains duplicated data.

2016-02-21 | E-GEOD-69071 | biostudies-arrayexpress

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

Project description:To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci. A 4 chips study of exponentially growing wild type E. coli strain MG1655 grown in LB rich media or after induction of the stringent response by serine hydroxamate for 30 min. Two technical replicates, Three biological replicates mixed prior hybridization on the chip.

2013-05-01 | E-GEOD-40304 | biostudies-arrayexpress

Comparative analysis of chrysanthemum transcriptome in response to infection of three viruses: Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X

Project description:Gene expression analysis of chrysanthemum infected with three different viruses including Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X have been performed using the chrysanthemum 135K microarray. Mock and each virus infected chrysanthemum plants were subjected for microarray analysis.

2015-01-01 | E-GEOD-55985 | biostudies-arrayexpress

Comprehensive transcriptional profiling analysis reveals candidate regulators in cold-stressed seedlings of Petunia hybrida

Project description:Investigation of gene expression level changes in Petunia hybrida seedlings subjected to cold at 2°C for 0.5 h, 2 h, 24 h and 5 d, compared to the CK. The custom-designed four-plex microarray with 72000 features was constructed based on the EST sequences generated in Breuillin's study together with all sequences of P.hybrida and P.axillaris available at Genbank, TIGR, and the Solanaceae genomics network SGN, which was ultimately composed by a set of 24816 non-redundant unique sequences (unigenes).The probe intensity files resulting from RNA hybridization were first read into R. Background Correction, quantile normalization and summarization were then performed using the Robust Multi-array Average (RMA) method included in Bioconductor Affy package based on the home made chip description library.

2015-01-15 | E-GEOD-64963 | biostudies-arrayexpress

Expression analysis of Lactococcus lactis NIAI712 and its plasmid cured variant

Project description:L. lactis NIAI712 carries five different plasmids, including an 8.7-kb plasmid designated pAG6. In this study, genome-wide expression profiles of the pAG6-cured variant was compared to the wild-type strain. Two samples of total RNA recovered from a wild-type culture of L. lactis NIAI712 and a pAG6-cured variant were examined

2013-08-31 | E-GEOD-48143 | 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