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SRP043590
Mus musculus
12 Downloadable Samples
Illumina HiSeq 2000
Description
Reprogramming intermediates (pre-iPSCs) were subjected to control DMSO, ascorbic acid (AA), 2i ( MAP kinase inhibitor + GSKinhibitor) or AA+2i conditions to assess conversion to the iinduced pluripotent stem cell state (iPSC) after 10days. Overall design: Pre-iPSC cells exposed to control DMSO, AA, 2i or AA+2i were harvested on day 2 for RNA sequencing after treatment, in biological triplicate.
Publication Title
Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 48 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Renal gene expression analysis was performed in mouse strains with different propensity to develop progressive chronic kidney disease (CKD) after subtotal nephrectomy: the FVB strain which is spontaneously highly predisposed to CKD and the C57BL/6 which is spontaneously not predisposed to CKD. Subtotal nephrectomy (Nx) is normally initially compensated by proliferative tissue repair (2 days after nephrectomy). After this initial proliferation follows a quiescent period (28 days after NX). Finally, specifically in the sensitive strain there is lesion onset (53 days after Nx). Gene expression was monitored on RNA from whole kidneys from different mouse strains Sham operated or Nephrectomised at three different time-points.
Publication Title
Signaling pathways predisposing to chronic kidney disease progression.
Sample Metadata Fields
Time
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
We used microarrays to detail the global program of gene expression during early hESC differentiation to mesendoderm using FBS, with and without RUNX1 depletion.
Publication Title
Transient RUNX1 Expression during Early Mesendodermal Differentiation of hESCs Promotes Epithelial to Mesenchymal Transition through TGFB2 Signaling.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 20 Downloadable Samples
- Illumina HiSeq 2500
Description
We identified 4,356 genes with expression differences associated with a high-fat diet, with 184 genes exhibiting a sex-by-diet interaction. Dietary fat dysregulated several pathways, such as cytokine-cytokine receptor interaction, chemokine signaling, and oxidative phosphorylation. Grant: Funding source: American Heart Association Grant number: 16PRE26420105 Title: The effect of maternal over-nutrition on obesity, epigenetics, and gene expression Awarded to Madeline Keleher Overall design: We performed RNA-seq in 21 total libraries, each with two mice of the same sex and diet pooled together (There were 6 low-fat-fed female libraries, 5 libraries of high-fat-fed females, 5 libraries of low-fat-fed males, and 5 libraries of high-fat-fed males). A 1x50 single read sequencing run was done on an Illumina HiSeq 2500 machine (Illumina Inc.)
Publication Title
A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Arabidopsis thaliana
- 47 Downloadable Samples
- Illumina HiSeq 2000
Description
Plant cell surface receptors sense microbial pathogens by recognizing microbial structures called pathogen or microbe-associated molecular patterns (PAMPs/MAMPs). There are two major types of plant pattern recognition receptors: 1. Leucine-rich repeat receptor proteins (LRR-RP) and LRR receptor kinases (LRR-RK) and 2. Plant receptor proteins and receptor kinases carrying ectopic lysin motifs (LysM-RP and LysM-RK). In this study, Arabidopsis thaliana responses to three different MAMPs, flg22, nlp20, chitin (C6), via their corresponding receptor types, FLS2 (LRR-RK), RLP23 (LRR-RP), CERK1 (LysM-RK) were compared. Our RNA-seq results indicate that a core set of defense-related genes can be activated through perception of different MAMPs. However, there are also notable differences in the transcriptional changes in response to the various elicitors; flg22 causes broader transcriptome changes than nlp20 and C6, and C6 does not cause late transcriptome changes. Overall design: Arabodopsis seedings were treated with water, flg22, nlp20, or C6 and collected after 1h, 6h and 24h. One sample before treatment was also collected. 4 biological repecates were performed.
Publication Title
Comparing Arabidopsis receptor kinase and receptor protein-mediated immune signaling reveals BIK1-dependent differences.
Sample Metadata Fields
Subject, Time
View Samples- Rattus norvegicus
- 12 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
Study on selective vulnerability of certain brain regions to oxidative stress. Here we selected 4 brain regions (hippocampal CA1 and CA3, cerebral cortex, and cerebellar granular layer) to study this phenomenon.
Publication Title
Genomic and biochemical approaches in the discovery of mechanisms for selective neuronal vulnerability to oxidative stress.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Drosophila Gene 1.1 ST Array (drogene11st)
Description
Coupling immunity and development is essential to ensure survival despite changing internal conditions in the organism. The metamorphosis of the fruit fly represents a striking example of drastic and systemic physiological changes that need to be integrated with the innate immune system. However, the mechanisms that coordinate development and immune cell activity in the transition from larva to adult in Drosophila remain to elucidate. The steroid hormone ecdysone is known to act as a key coordinator of metamorphosis. This hormone activates a nuclear receptor, the Ecdysone Receptor (EcR), which acts as a heterodimer with its partner Ultraspiracle (USP). Together, they activate the transcription of primary response genes, which in turn activate the transcription of a battery of late response genes. We have revealed that regulation of macrophage-like cells (hemocytes) by the steroid hormone ecdysone is essential for an effective innate immune response over metamorphosis. We have shown that in response to ecdysone signalling, hemocytes rapidly up regulate actin dynamics, motility and phagocytosis of apoptotic corpses, and acquire the ability to chemotax to damaged epithelia. Most importantly, individuals lacking ecdysone-activated hemocytes are defective in bacterial phagocytosis and are fatally susceptible to infection by bacteria ingested at larval stages, despite the normal systemic production of antimicrobial peptides. This decrease in survival is comparable to the one observed in pupae lacking immune cells altogether, indicating that ecdysone-regulation is essential to hemocyte immune functions and survival after infection.
Publication Title
Steroid hormone signaling is essential to regulate innate immune cells and fight bacterial infection in Drosophila.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Gender dimorphism exists in the physiological response to diet and other environmental factors. Trans-hydrogenated fatty acid (TFA) intake is associated with an increase in coronary heart disease (CHD), and gender differences in the incidence of CHD are well documented. Neonatal administration of Monosodium Glutamate (MSG) causes stunted heart growth and hypoplasticity; and gender dimorphism at the growth hormone axis has been demonstrated in MSG-treated rodents. The identification of gender dimorphism in cardiac nutrigenomics may provide the basis for gender-specific medicine in the future.
Publication Title
Sex-dimorphism in cardiac nutrigenomics: effect of trans fat and/or monosodium glutamate consumption.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 72 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Ovarian cancer is the most lethal malignancy in the United States. In the year 2012, there will be an estimated 22,280 new cases and 15,500 deaths from ovarian cancer in the country (Siegel et al., 2012). While studies on ovarian cancer pathogenesis were mainly focused on the epithelial component of the tumor, understanding in the role of cancer associated fibroblasts (CAFs) in ovarian cancer progression is limited. We hypothesized that comparing the gene expression profiles of different components from laser capture microdissected ovarian tissue will allow us to identify an ovarian CAFs specific gene signature which accounts for the supportive role of CAFs in ovarian cancer progression. In this study, gene expression profiling was completed for 31 cancer stroma samples and 32 samples of epithelial component from high grade serous ovarian cancer patients. 8 microdissected normal ovarian stroma and 6 normal human ovarian surface epithelium (HOSE) samples were also included in the study. By comparing the expression data from cancer stroma against that from normal stroma, cancer cells and HOSE, we identified a set of differential expressed genes in ovarian CAFs which showed correlation with cancer patient survival. Further study on these genes can reveal their roles in ovarian cancer progression and pathogenesis. Ultimately, ovarian CAFs specified genes identified in this study may aid in the classification and enhancement of patient outcome.
Publication Title
TGF-β modulates ovarian cancer invasion by upregulating CAF-derived versican in the tumor microenvironment.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
We used microarrays to detail the global programme of gene expression during early hESC differentiation to Mesendoderm using FBS.
Publication Title
Lineage-Specific Early Differentiation of Human Embryonic Stem Cells Requires a G2 Cell Cycle Pause.
Sample Metadata Fields
Sex, Cell line, Time
View Samples