Filters
Technology
Platform
GSE81416
Homo sapiens
1 Downloadable Sample
Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Inflammatory breast cancer (IBC) is the most aggressive form of breast cancer. Treatment options are limited and the mechanisms underlying its aggressiveness are poorly understood. Intermittent hypoxia (IH) causes oxidative stress and is emerging as important regulator of tumor metastasis. Vessels in IBC tumors were shown to be immature, which is a primary cause of IH. We therefore investigated the relevance of IH for the modulation of gene expression in IBC cells in order to assess IH as potential regulator of IBC aggressiveness. Gene array analysis of IBC cells following chronic IH (45-60 days) demonstrated increased expression of pro-metastatic genes of the extracellular matrix, such as tenascin-C (TNC; an essential factor of the metastatic niche) and matrix metalloproteinase 9 (MMP9), and of pro-inflammatory processes, such as cyclooxygenase-2 (COX-2). Investigating the oxidative stress-dependent regulation of TNC, we found a gradual sensitivity on mRNA and protein levels. Oxidative stress activated NF-E2-related factor 2 (Nrf2), c-Jun N-terminal kinase (JNK), c-Jun and nuclear factor B (NF-B), but TNC upregulation was only dependent on NF-B activation. Pharmacological inhibition of inhibitor of NF-B (IB) phosphorylation as well as overexpression of IB prevented TNC, MMP9 and COX-2 induction, whereas the pro-inflammatory cytokine interleukin-1 (IL-1) increased their expression levels. Analysis of the gene array data showed NF-B binding sites for 64% of all upregulated genes, linking NF-B and IH-dependent regulation of pro-metastatic gene expression in IBC cells. Our results provide a first link between intermittent hypoxia and pro-metastatic gene expression in IBC cells, revealing a putative novel mechanism for the high metastatic potential of IBC.
Publication Title
Intermittent hypoxia confers pro-metastatic gene expression selectively through NF-κB in inflammatory breast cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data.
Publication Title
Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
Illumina HiSeq 4000
Description
RNA transcriptome sequencing analysis was performed in SGC-7901 cells that were transfected with ENST00000431060 shRNA or control shRNA Overall design: mRNA profiles of SGC-7901 cells transfected with ENST00000431060 shRNA or control shRNA
Publication Title
lncRNA GCAWKR Promotes Gastric Cancer Development by Scaffolding the Chromatin Modification Factors WDR5 and KAT2A.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaHiSeq2500
Description
To identify potential mRNA targets of FTO whose m6A levels are affected by FTO in acute myeloid leukemia (AML) cells, we conducted m6A-seq for messenger RNAs isolated from AML cells with and without forced expression of FTO. Overall design: We retrovirally transduced MSCV-PIG-FTO (i.e., human FTO) or MSCV-PIG (i.e., CTRL/Control) into human MONOMAC-6/t(9;11) AML cells and then selected individual stable clones under selection of puromuycin (0.5ug/ml). Four stable lines including two each FTO-overexpressing lines (i.e., FTO+ 1 and FTO+ 2; or FTO_1 and FTO_2) and control lines (i.e., WT 1 and WT 2; or Ctrl_1 and Ctrl_2) were selected for genome-wide m6A-sequencing (m6A-Seq) assays. The m6A-seq procedure was performed as detailed in Dominissini's method (Dominissini D., et al. Nat Protocols. 2013; 8: 176-189.). Polyadenylated RNA was extracted using FastTrack MAG Maxi mRNA isolation kit (Life technology). RNA fragmentation Reagents (Ambion) was used to randomly fragment RNA. M6A antibody (Synaptic Systems) was applied for m6A pull down. And final library preparation was constructed by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Final library was quantified by BioAnalyzer High Sensitivity DNA chip then deeply sequenced on the Illumina HiSeq 2500.
Publication Title
FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N<sup>6</sup>-Methyladenosine RNA Demethylase.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
To identify the expression of mRNAs after knockdown of FTO, we performed RNA-Seq in MA9.3ITD cells with or without knockdown of FTO. Overall design: We lentivirally transduced pLKO.1-shFTO (i.e., shFTO) or pLKO.1 empty vertor (i.e., shNS) into human MA9.3ITD (human CD34+ hematopoietic stem/progenetor cells stably infected by MLL-AF9 and FLT3-ITD) AML cells and then selected positively infected cells under selection of puromuycin (0.5ug/ml). The knockdown efficiency was confirmed by qPCR and western. Two stable lines including one FTO-knockdown cell line (i.e., shFTO) and one control line (i.e., shNS) were selected for RNA-Seq. Polyadenylated RNA was extracted using FastTrack MAG Maxi mRNA isolation kit (Life technology). RNA fragmentation Reagents (Ambion) was used to randomly fragment RNA. And final library preparation was constructed by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Final library was quantified by BioAnalyzer High Sensitivity DNA chip then deeply sequenced on the Illumina HiSeq 2500.
Publication Title
FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N<sup>6</sup>-Methyladenosine RNA Demethylase.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
To identify potential mRNA targets of FTO whose m6A levels are influenced in acute myeloid leukemia (AML) cells, we conducted m6A-seq for mRNA isolated from MA9.3ITD cells with and without knockdown of FTO Overall design: We lentivirally transduced pLKO.1-shFTO (i.e., shFTO) or pLKO.1 empty vertor (i.e., shNS) into human MA9.3ITD (human CD34+ hematopoietic stem/progenetor cells stably infected by MLL-AF9 and FLT3-ITD) AML cells and then selected positively infected cells under selection of puromuycin (0.5ug/ml). Two stable lines including one FTO-knockdown cell line (i.e., shFTO) and one control line (i.e., shNS) were selected for genome-wide m6A-sequencing (m6A-Seq) assays. The m6A-seq procedure was performed as detailed in Dominissini's method (Dominissini D., et al. Nat Protocols. 2013; 8: 176-189.). Polyadenylated RNA was extracted using FastTrack MAG Maxi mRNA isolation kit (Life technology). RNA fragmentation Reagents (Ambion) was used to randomly fragment RNA. M6A antibody (Synaptic Systems) was applied for m6A pull down. And final library preparation was constructed by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Final library was quantified by BioAnalyzer High Sensitivity DNA chip then deeply sequenced on the Illumina HiSeq 2500.
Publication Title
FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N<sup>6</sup>-Methyladenosine RNA Demethylase.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq from R-2HG sensitive leukemia cells treated with R-2HG or PBS. Overall design: With MTT assays, we identified R-2HG exhibits an anti-leukemia function. We conducted RNA-Seq in the two sensitive cells (NOMO-1 and MA9.3ITD) with R-2HG or without R-2HG treatment for 48 hours to investigate which genes/a-ketoglutarate-dependent dioxygenases/signaling pathways are responsible for the anti-leukemia function of R-2HG. For each group, there are three duplicates.
Publication Title
R-2HG Exhibits Anti-tumor Activity by Targeting FTO/m<sup>6</sup>A/MYC/CEBPA Signaling.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Oryza sativa
- 216 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice flag leaf at heading date from 210 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In the study, we attempted to construct the regulatory network by identifying putative regulators and the respective targets using an eQTL guided co-expression analysis with a recombinant inbred line population of rice.
Publication Title
An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
NADPH-cytochrome P450 reductase (CPR) is important for the functions of many enzymes, such as microsomal cytochrome P450 (P450) monooxygenases and heme oxygenases. Two mouse models with deficient CPR expression in adults were recently generated in this laboratory: liver-Cpr-null (with liver-specific Cpr deletion) (Gu et al., J. Biol. Chem., 278, 2589525901, 2003) and Cpr-low (with reduced CPR expression in all organs examined) (Wu et al. J. Pharmacol. Expt. Ther. 312, 35-43, 2005). The phenotypes included a reduced serum cholesterol level and an induction of hepatic P450 in both models, and hepatomegaly and fatty liver in the liver-Cpr-null mouse alone. Our aim was to identify hepatic gene-expression changes related to these phenotypes. Cpr-lox mice, which have normal CPR expression (Wu et al., Genesis, 36, 177-181, 2003.), were used as the control in microarray analysis. A detailed analysis of the gene-expression changes in lipid metabolism and transport pathways revealed potential mechanisms, such as an increased activation of constitutive androstane receptor (CAR) and a decreased activation of peroxisomal proliferators activated receptor alpha (PPAR-gamma) by precursors of cholesterol biosynthesis, that underlie common changes (e.g., induction of multiple P450s and inhibition of genes for fatty acids metabolism) in response to CPR-loss in the two mouse models. Moreover, we also uncovered model-specific gene-expression changes, such as the induction of a lipid translocase (CD36 antigen) and the suppression of carnitine O-palmitoyltransferase 1 (CPT1a) and acyl-CoA synthetase long-chain family member 1 (Acsl1), that are potentially responsible for the severe hepatic lipidosis observed in liver-Cpr-null, but not Cpr-low mice.
Publication Title
Hepatic gene expression changes in mouse models with liver-specific deletion or global suppression of the NADPH-cytochrome P450 reductase gene. Mechanistic implications for the regulation of microsomal cytochrome P450 and the fatty liver phenotype.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Despite many studies over a decade, it still remains ambiguous as to the real biological effects induced by radiofrequency electromagnetic fields (RF EMF). Epidemiological studies indicates that long-term exposure to EMF could increase the risk of breast cancer. Some reports have showed that in vitro EMF exposures change cellular gene expression. In this study, we investigated global gene expression responses to RF EMF simulating the Global System for Mobile Communications (GSM) 1800 MHz signal in human breast cancer cell line MCF-7 using transcriptomic approaches.
Publication Title
Effects of global system for mobile communications 1800 MHz radiofrequency electromagnetic fields on gene and protein expression in MCF-7 cells.
Sample Metadata Fields
Cell line
View Samples