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Mus musculus
12 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Amplification of MYCN is the most prominent genetic marker of high-stage neuroblastoma, a childhood tumor originating from the neural crest. We generated a cell line (mNB-A1) from tumors developed in transgenic mouse and treated these cells with DMSO (n=6), the BRD4-inhibitor JQ1 (n=3) or the AURKA-inhibitor MLN8237 (n=3) for 24 h.
Publication Title
A Cre-conditional MYCN-driven neuroblastoma mouse model as an improved tool for preclinical studies.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Amplification of MYCN is the most prominent genetic marker of high-stage neuroblastoma, a childhood tumor originating from the neural crest.
Publication Title
A Cre-conditional MYCN-driven neuroblastoma mouse model as an improved tool for preclinical studies.
Sample Metadata Fields
Cell line
View Samples- Oryza sativa
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
We advance a three gene model of arsenate tolerance in rice based on testing root growth of 108 recombinant inbred lines (RILs) of the Bala x Azucena population. Marker genotype at 3 loci determined arsenate tolerance in 99% of RILs tested. Interestingly, plants must inherit 2, but any two alleles from the tolerant parent (Bala) to have the tolerant phenotype. Challenging the Affymetrix GeneChip Rice Genome array with Azucena and Bala RNA isolated from control and arsenate treated plants revealed 592 genes 2 fold-upregulated by arsenate and 696 downregulated. The array data was also used to identify which genes are expressed within the three target loci.
Publication Title
Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Oryza sativa
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer.
Publication Title
A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We used microarrays to establish whether EBF1 and Pax5 repress similar or unique genes. We found that EBF1 uniquely represses the expression of the T-lineage transcription factor Gata3.
Publication Title
Transcriptional repression of Gata3 is essential for early B cell commitment.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 42 Downloadable Samples
Description
TCF7L2 regulates multiple metabolic pathways in hepatocytes through a transcriptional network involving HNF4a Overall design: For the identification of Tcf7l2 target genes using a RNA-seq timecourse, and for identifying the binding sites of Tcf7l2 and Hnf4a, Tcf7l2 was silenced in rat H4IIE hepatocytes using siRNA for Tcf7l2 with a scrambled siRNA as control. Treatment times for RNA-seq samples were 3, 6, 9, 12, 15, 18, 48, and 96 hours, and for ChIP-seq samples 15 h. RNA-seq timecourse was performed in duplicate or triplicate, and the ChIP-seq in duplicate for Tcf7l2 and in singlicate for Hnf4a. The H4IIE-specific transcriptome was defined from an independent set of pooled 24 h siRNA treated samples (N=3 for siRNA for Tcf7l2 and N=3 for scrambled siRNA).
Publication Title
The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 22 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip, Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Tumor entrained neutrophils inhibit seeding in the premetastatic lung.
Sample Metadata Fields
Sex, Specimen part, Disease, Treatment
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip, Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Primary tumors have been shown to prepare distal organs for later colonization of metastatic cells by stimulating organ-specific infiltration of bone marrow-derived cells. Here we demonstrate that neutrophils accumulate in the lung prior to the arrival of metastatic cells in mouse models of breast cancer. Tumor-entrained neutrophils (TENs) inhibit metastatic seeding in the lungs by generating H2O2, and tumor-secreted CCL2 is a critical mediator of optimal anti-metastatic entrainment of G-CSF-stimulated neutrophils. TENs are present in the peripheral blood of breast cancer patients prior to surgical resection but not in healthy individuals. Thus, while tumor-secreted factors contribute to tumor progression at the primary site, they concomitantly induce a neutrophil-mediated inhibitory process at the metastatic site.
Publication Title
Tumor entrained neutrophils inhibit seeding in the premetastatic lung.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples
GSE30887- Mus musculus
- 10 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Primary tumors have been shown to prepare distal organs for later colonization of metastatic cells by stimulating organ-specific infiltration of bone marrow-derived cells. Here we demonstrate that neutrophils accumulate in the lung prior to the arrival of metastatic cells in mouse models of breast cancer. Tumor-entrained neutrophils (TENs) inhibit metastatic seeding in the lungs by generating H2O2, and tumor-secreted CCL2 is a critical mediator of optimal anti-metastatic entrainment of G-CSF-stimulated neutrophils. TENs are present in the peripheral blood of breast cancer patients prior to surgical resection but not in healthy individuals. Thus, while tumor-secreted factors contribute to tumor progression at the primary site, they concomitantly induce a neutrophil-mediated inhibitory process at the metastatic site.
Publication Title
Tumor entrained neutrophils inhibit seeding in the premetastatic lung.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Homo sapiens
- 25 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background. Differential gene expression in adipose tissue during diet-induced weight loss followed by a weight stability period is not well characterized. Markers of these processes may provide a deeper understanding of the underlying mechanisms. Objective. To identify differentially expressed genes in human adipose tissue during weight loss and weight maintenance after weight loss. Design. RNA from subcutaneous abdominal adipose tissue from nine obese subjects was obtained and analyzed at baseline, after weight reduction on a low calorie diet (LCD), and after a period of group therapy in order to maintain weight stability. Results. Subjects lost 18.8 + 5.4% of their body weight during the LCD and maintained this weight during group therapy. Insulin sensitivity (HOMA) improved after weight loss with no further improvement during weight maintenance. Cyclin-dependent kinase inhibitor 2B (CDKN2B) and JAZF zinc finger 1 (JAZF1), associated with type 2 diabetes, were downregulated. We could also confirm the downregulation of candidates for obesity and related traits, such as tenomodulin (TNMD) and matrix metallopeptidase 9 (MMP9), with weight loss. The expression of other candidates, such as cell death-inducing DFFA-like effector A (CIDEA) and stearoyl-CoA desaturase (SCD) were upregulated during weight loss but returned to baseline levels during weight maintenance. Conclusion. Genes in the adipose tissue are differentially expressed during weight loss and weight maintenance after weight loss. Genes that show sustained regulation may be of potential interest as markers of the beneficial effects of weight loss whereas others seem to be primarily involved in the process of weight loss itself.
Publication Title
Differential gene expression in adipose tissue from obese human subjects during weight loss and weight maintenance.
Sample Metadata Fields
Sex, Age
View Samples