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GSE46495
Mus musculus
30 Downloadable Samples
Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Fasting is the process of metabolic adaption to food deprivation that is taking place in most organisms, e.g. during the daily resting phase in mammals. Furthermore, in biomedical research fasting is used in most metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the molecular players in fasting. In this study we investigated the transcriptome signature of white adipose tissue, liver, and skeletal muscle in 24 hours fasted mice (and chow fat controls) using Affymetrix whole-genome microarrays.
Publication Title
Metabolite and transcriptome analysis during fasting suggest a role for the p53-Ddit4 axis in major metabolic tissues.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Here we investigated the effect of stable knock-down of the NAA-catabolizing enzyme, Aspartoacylase (Aspa), on global gene expression in a brown adipocyte cell line.
Publication Title
N-acetylaspartate catabolism determines cytosolic acetyl-CoA levels and histone acetylation in brown adipocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Keratinocyte growth factor (KGF, fibroblast growth factor-7) is a fibroblast-derived mitogen, which stimulates proliferation of epithelial cells. The expression of KGF by dermal fibroblasts is induced following injury and it promotes wound repair. However, the role of KGF in cutaneous carcinogenesis and cancer progression is not known. We have examined the role of KGF in progression of squamous cell carcinoma (SCC) of the skin.
Publication Title
Keratinocyte growth factor induces gene expression signature associated with suppression of malignant phenotype of cutaneous squamous carcinoma cells.
Sample Metadata Fields
Specimen part, Disease
View Samples- Mus musculus
- 14 Downloadable Samples
Illumina HiSeq 2000
Description
Expression profiling of hepatocytes-derived ductal cells with properties intermediate between mature hepatocytes and cholangiocytes Overall design: Chimeric adult mice were generated where mature hepatocytes were marked with a fluorescent red marker. Chronic injury was induced for ~6weeks and three cell types were isolated by FACS (Influx, BD) for expression analysis by RNAseq based on cell surface phenotype and origin: hepatocytes (n=3), hepatocyte-derived oval cells (1c3+, n=5), and cholangiocyte-derived oval cells (1c3+, n=5).
Publication Title
Bipotential adult liver progenitors are derived from chronically injured mature hepatocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
We used wild-type 129 mice to understand the mechanism of action behind SRT3025’s hematopoiesis-enhancing effect. Transcriptome analysis of cKit+ Sca1+ Lin- cells (KSL) cells discovered that a list of genes changed their expression levels significantly after SRT3025 administration in wild-type mice. Most notably, the cell cycle regulator p21 was down-regulated by 2.1 fold after SRT3025 administration. It is possible that the transcriptional suppression of p21 by SRT3025 might contribute to the compound’s beneficial effects on hematopoiesis. It has to be pointed out that, since our transcriptome analysis was limited to hematopoietic stem and progenitor cell population, we cannot rule out the possibility that SRT3025 works through the regulation of other cells such as certain important HSC niche components. The HSC niche is known to regulate stem cell pool size. Among the other genes suppressed by SRT3025, Thbs1 and Fosl2 encode thrombospondin 1 and Fos-like antigen 2, respectively. Both proteins are components of the HSC niche. Overall design: The goal of this study is to investigate gene expression changes in wild-type 129 mice in response to SRT3025 treatment. The study focuses on bone marrow cKit+ Sca1+ Lin- cells (representing hematopoietic stem and progenitor cells). These cells were sorted twice by FACS to ensure the purity. Cells of interest were collected in Trizol. RNA were isolated using RNAeasy mini prep kit and mRNAs were positively selected using oligo(dT)- Dynobeads. Then RNAseq libraries were then made using Illumina TruSeq RNA Sample Prep Kit and sequeced on an Illumina HiSeq 2000 genome analyzer.
Publication Title
The Sirt1 activator SRT3025 expands hematopoietic stem and progenitor cells and improves hematopoiesis in Fanconi anemia mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
We report here an improved protocol to reprogram mouse gallbladder cells (GBCs) into pancreatic beta cells. To fully understand the extent of reprogramming, mRNA was extracted from FACS-purified MIP-GFP positive insulin-producing cells (namely rGBC2) for RNA-seq after 10-days of in vitro reprogramming. The global gene expression profile of rGBC2 was compared with that of primary gallbladder cells, GBC reprogrammed with the rGBC1 protocol (Hickey et al., 2013) and mouse pancreatic ß cells (Benner et al., 2014). We show that rGBC2 from four independent cell batches showed a unique gene expression phenotype. Compared with the rGBC1 protocol, rGBC2 expressed many additional pancreatic ß cell genes, suppressed many gallbladder genes and resulted in an expression profile closer to pancreatic ß cells. Overall design: Gene expression profiling of galbladder reprogrammed, insulin positive cells using the improved reprogramming protocol
Publication Title
Efficient generation of pancreatic β-like cells from the mouse gallbladder.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
The goal of this study was to determine the transcriptional changes associated with breast cancer cells undergoing vascular mimicry in a 3D assay. Two breast cancer cell lines were plated on matrigel in the presence or absence of serum. MDA-MB-231 cells undergo vascular mimicry on matrigel in the absence of serum, MDA-MB-453 cells do not. Overall design: Four samples were analyzed. MDA-MB-231 and MDA-MB-453 cells were plated for 24 hours on matrigel in the presence or absence of serum. MDA-MB-231 cells undergo vascular mimicry when plated on matrigel in the absence of serum, while MDA-MB-453 cells do not.
Publication Title
ZEB1-repressed microRNAs inhibit autocrine signaling that promotes vascular mimicry of breast cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 5 Downloadable Samples
- IlluminaHiSeq2000
Description
Inhibition of SET by siRNA or SET antagonist and CIP2A by siRNA can downregulate c-MYC and c-MYC target genes. Overall design: Cells were treated with a SET antagonist (1µMOP449) for 12 hours, or siRNA for 48 hours.
Publication Title
Targeting c-MYC by antagonizing PP2A inhibitors in breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina Genome Analyzer II
Description
Examination of Pin1-regulated Myc target genes in a human breast epithelial cell line. Overall design: Two samples: control GFP-expressing MCF10A-Myc cells and Pin1-expressing MCF10A-Myc cells.
Publication Title
Pin1 regulates the dynamics of c-Myc DNA binding to facilitate target gene regulation and oncogenesis.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina Genome Analyzer II
Description
miR-132 and miR-212 are structurally-related microRNAs that have been found to exert powerful modulatory effects within the central nervous system (CNS). Notably, these microRNAs are tandomly processed from the same non-coding transcript, and share a common seed sequence: thus it has been difficult to assess the distinct contribution of each microRNA to gene expression within the CNS. Here, we employed a combination of conditional knockout and transgenic mouse models to examine the contribution of the miR-132/212 gene locus to learning and memory, and then to assess the distinct effects that each microRNA has on hippocampal gene expression. Using a conditional deletion approach, we show that miR-132/212 double knockout mice exhibit significant cognitive deficits in spatial memory, recognition memory, and in tests of novel object recognition. Next, we utilized transgenic miR-132 and miR-212 overexpression mouse lines and the miR-132/212 double knockout line explore the distinct effects of these two miRNAs on the transcriptional profile of the hippocampus. Illumina sequencing revealed that miR-132/212 deletion increased the expression of 1,138 genes; Venn analysis showed that 96 of these genes were also downregulated in mice overexpressing miR-132. Of the 58 genes that were decreased in animals overexpressing miR-212, only four of them were also increased in the knockout line. Functional gene ontology analysis of downregulated genes revealed significant enrichment of genes related to synaptic transmission, neuronal proliferation, and morphogenesis, processes known for their roles in learning, and memory formation. These data, coupled with previous studies, firmly establish a role for the miR-132/212 gene locus as a key regulator of cognitive capacity. Further, although miR-132 and miR-212 share a seed sequence, these data indicate that these miRNAs do not exhibit strongly overlapping mRNA targeting profiles, thus indicating that, these two genes may function in a complex, non-redundant manner to shape the transcriptional profile of the CNS. The dysregulation of miR-132/212 expression could contribute to signaling mechanisms that are involved in an array of cognitive disorders Overall design: Hippocampal mRNA was isolated from CaMKII-Cre::miR-132/212f/f, tTA::miR132, and tTA::miR212 animals, as well as their respective nontransgenic controls. cDNA from six animals was pooled into three independent biological replicates for each. Libraries were prepared according to the Illumina TruSeqTM Sample Preparation Guide and sequenced using an Illumina Genome Analyzer II. Sequences were aligned to the UCSC mm9 reference genome using Bowtie v0.12.7 and custom R scripts. The sequence data have been submitted to the NCBI Short Read Archive with accession number in progress. Relative abundance was measured in Fragments Per Kilobase of exon per Million fragments mapped using Cufflinks v1.2.
Publication Title
Targeted deletion of miR-132/-212 impairs memory and alters the hippocampal transcriptome.
Sample Metadata Fields
Cell line, Subject
View Samples