Filters
Technology
Platform
GSE44097
Homo sapiens
12 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To validate the suitability of two commonly used colorectal cancer cell lines, DLD1 and SW480, as model systems to study colorectal carcinogenesis, we treated these cell lines with -catenin siRNA and identified -catenin target genes using DNA microarrays. The list of identified target genes was compared to previously published -catenin target genes found in the PubMed and the GEO databases.
Publication Title
Comprehensive analysis of β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling.
Sample Metadata Fields
Cell line, Treatment
View Samples- Rattus norvegicus
- 15 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
The transcriptional effects of urocortin I, urocortin II and tempol were compared to saline treatment in a rat model of in vivo coronary artery occlusion model of ischaemia/reperfusion injury of 25 min ischaemia and 2 hr reperfusion. <br></br>The treatment groups were as follows (i) sham operation or LAD occlusion with infusion of (ii) saline, (iii) 15 ?g/kg Ucn I, (iv) 15 ?g/kg Ucn II and (v) 100 mg/kg tempo infused just prior to reperfusionl.<br></br>Following 2 hr reperfusion the left ventricle was removed, snap frozen, followed by RNA extraction.
Publication Title
New targets of urocortin-mediated cardioprotection.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject, Compound, Time
View Samples- Mus musculus
- 11 Downloadable Samples
Illumina HiSeq 2500
Description
Cancer resistance is a major cause for longevity of the naked mole-rat. Recent liver transcriptome analysis in this animal compared to wild-derived mice revealed higher expression of alpha2-macroglobulin (A2M) and cell adhesion molecules, which contribute to the naked mole-rat's cancer resistance. Notably, A2M is known to dramatically decrease with age in humans. We hypothesize that this might facilitate tumour development. Here we found that A2M modulates tumour cell adhesion, migration and growth by inhibition of tumour promoting signalling pathways, e.g. PI3K / AKT, SMAD and up-regulated PTEN via down-regulation of miR-21, in vitro and in tumour xenografts. A2M increases the expression of CD29 and CD44 but did not evoke EMT. Transcriptome analysis of A2M-treated tumour cells, xenografts and mouse liver demonstrated a multifaceted regulation of tumour promoting signalling pathways indicating a less tumorigenic environment mediated by A2M. By virtue of these multiple actions the naturally occurring A2M has strong potential as a novel therapeutic agent. Overall design: 11 samples: 5 treated with PBS, 6 treated with A2M
Publication Title
The anti-tumorigenic activity of A2M-A lesson from the naked mole-rat.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The organization of mammalian DNA replication is poorly understood. We have produced genome-wide high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal and embryonic stem cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy number variations during S phase obtained using either high-density oligonucleotide tiling arrays or massively-parallel sequencing to produce replication timing profiles. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation where replication forks progress unidirectionally from origins that can be hundreds of kilobases away. Absence of initiation in one transition region is shown at the molecular level by SMARD analysis. Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarter of S phase and that ES cells replicate a larger proportion of their genome in early S phase than erythroid cells. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid firing origins are located near moderately expressed genes and that late firing origins are located far from genes.
Publication Title
Predictable dynamic program of timing of DNA replication in human cells.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 99 Downloadable Samples
- IlluminaHiSeq2000, IlluminaHiScanSQ
Description
The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR. Overall design: 105 samples were selected from the DrugMatirx tissue/RNA bank that is now owned by the National Toxicology Program (NTP). The samples were split into 2 sets, training and test, to allow for the evaluation of classifiers derived from the data. There were 63 samples in the training set and 42 in the test set. Of the 63 samples in the training set 45 were derived from rats treated with test agent and 18 were control samples (3 sets of 6). 39 of the test set samples were derived from test agent treated animals and 6 were from vehicle and route matched controls. Five MOAs were represented in the training set and 4 MOAs were in the test set. Two of the MOAs were duplicated from the test set and two were without representation in the training set. For each test agent there were three rats treated, in accordance with the common practice in the field of toxicology. For each MOA there were three representative test agents to ensure adequate power for detecting the MOA signatures. 6 samples from the training set had duplicate libraries sequenced and duplicate sequencing runs for the first library. DrugMatrix, National Toxicology program (NTP) Sequencing was carried out in Dr. Charles Wang's Functional Genomics Core at City of Hope Comprehensive Cancer Center, Duarte, CA
Publication Title
Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in normal eukaryotic cellular function. Here, we characterized the metabolic and transcriptional properties of A549 lung cancer cells and their isogenic mitochondrial DNA (mtDNA)-depleted rho zero counterparts grown in cell culture and as tumor xenografts in immune-deficient mice. A manuscript summarizing our conclusions is under review.
Publication Title
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Expression of mutant lamins in human muscle causes muscular dystrophy. We have generated a drosophila model that expresses mutant lamins, modeled after those that cause disease in humans.
Publication Title
Myopathic lamin mutations cause reductive stress and activate the nrf2/keap-1 pathway.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Synthesis and anticancer properties of water-soluble zinc ionophores.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We have demonstrated that water-soluble zinc ionophores can be administered to mice at relatively high doses and inhibit the growth of A549 lung cancer cells grown in xenograft models. Gene expression profiles of tumor specimens harvested from mice four hours after treatment confirmed that the activation of stress responsive genes occurs in vivo. These findings lead us to propose that the pharmacologic delivery of zinc to tumors using water solubilized ionophores is a potential approach to cancer therapy.
Publication Title
Synthesis and anticancer properties of water-soluble zinc ionophores.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We have shown that water solubilized versions of a zinc ionophore increase intracellular concentrations of free zinc and have antiproliferative activity in exponential phase A549 lung cancer cultures. The gene expression profiles of A549 lung cancer cultures treated with the lead compound PCI-5002 reveal the activation of stress response pathways. Medium supplementation with zinc (25 M) led to activation of additional oxidative stress response as well as apoptotic pathways. We propose that the pharmacologic delivery of zinc to tumors using water solubilized ionophores is a potential approach to cancer therapy.
Publication Title
Synthesis and anticancer properties of water-soluble zinc ionophores.
Sample Metadata Fields
No sample metadata fields
View Samples