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GSE111443
Arabidopsis thaliana
16 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Regulation of genes in shoots and roots and Arabidopsis in response to Zn-deficiency in wild-type and hma2 hma4 mutants plants
Publication Title
Systemic Upregulation of MTP2- and HMA2-Mediated Zn Partitioning to the Shoot Supplements Local Zn Deficiency Responses.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Comparison of transcriptional profile of TCR stimulated P14-TCR wild-type and P14-PKD2 null murine lymph node cells
Publication Title
Protein kinase D2 has a restricted but critical role in T-cell antigen receptor signalling in mature T-cells.
Sample Metadata Fields
Specimen part
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
- 36 Downloadable Samples
- IlluminaHiSeq1500
Description
To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.
Publication Title
Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In cytotoxic T cells (CTL), Protein Kinase B /Akt is activated by the T cell antigen receptor (TCR) and the cytokine Interleukin 2 (IL2), in part by phosophorylation of Akt by Phospholipid dependent kinase 1 (PDK1).
Publication Title
Protein kinase B controls transcriptional programs that direct cytotoxic T cell fate but is dispensable for T cell metabolism.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Comparison of transcriptional profile of CD8 cytotoxic T lymphocytes terated with the mTORC1 inhibitor rapamycin or the mTOR inhibitor KU-0063794 and comparison with proteomic analysis.
Publication Title
The cytotoxic T cell proteome and its shaping by the kinase mTOR.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Caenorhabditis elegans
- 20 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: The goal of this study is to understand how dbl-1, which is made primarily in neurons, and hrg-7, which is exclusively made in the intestine, contribute to systemic heme homeostasis. Methods: mRNA profiles of late L4 dbl-1(nk3) and hrg-7(tm6801) mutant C. elegans fed OP50 E. coli or OP50 + 50µM heme were compared to mRNA profiles from wildtype (WT) broodmates. Profiles were generated with single-end 50 base reads obtained using Illumina’s HiSeq 2500. Bioinformatics quality control was performed followed by alignment of reads to the ce10 reference genome using Tophat2, version 2.1.0. We found differentially expressed genes using Cufflinks 2, version 2.2.1 with a cutoff of 0.05 on False Discovery Rate (FDR). Results: We found a substantial overlap of genes regulated by both dbl-1 and hrg-7, including 49 heme-responsive genes (hrgs) in low heme (OP50) and 11 hrgs in high heme (OP50 + 50µM). Additionally, our data indicate crosstalk between dbl-1 and hrg-7 signaling. dbl-1 directly regulates hrg-7 expression, while hrg-7 regulates three components of the dbl-1 signaling pathway. Conclusions: Our study demonstrates that communication between the neuron and intestine is essential for heme homeostasis. Specifically, we report that HRG-7 functions as a secreted signaling factor which communicates intestinal heme status with extraintestinal tissues by integrating a DBL-1/BMP -dependent response from the neurons to transcriptionally regulate genes involved in heme homeostasis. Cellular requirements for heme are fulfilled by a cell’s internal capacity to synthesize its own heme in a cell-autonomous manner. However, growing evidence in vertebrates predicts that cellular heme levels in animals are not only maintained by heme synthesis, but also by distally located proteins that could signal systemic heme requirements to an inter-organ heme trafficking network through cell-nonautonomous regulation. Using C. elegans, a genetically and optically amenable animal model for visualizing heme-dependent signaling, we show that HRG-7, an aspartic protease homolog, mediates inter-organ signaling between the intestine and neuron. Loss of hrg-7 results in robust expression of intestinal heme importers and, remarkably, this occurs even under heme replete conditions when such transporters are not normally expressed. HRG-7 functions as a secreted signaling factor, independent of a functional enzymatic active site, and communicates intestinal heme status with extraintestinal tissues by integrating a DBL-1/BMP -dependent response from the neurons to transcriptionally regulate intestinal heme homeostasis. Given the evidence indicating that mechanisms of heme transport are conserved across metazoa, it is conceivable that the cell-nonautonomous signaling framework that we uncovered in C. elegans may have functional relevance for inter-organ regulation of iron and heme metabolism in humans. Overall design: Comparison of mRNA profiles from dbl-1(nk3) mutant C. elegans vs. wildtype (WT) broodmates and hrg-7(tm6801) mutants vs (WT) broomates fed OP50 E. coli or OP50 + 50µM heme. Biological duplicates were analyzed for dbl-1(nk3) mutants and (WT) broodmates. Biological triplicates were analyzed for hrg-7(tm6801) mutants and (WT) broodmates.
Publication Title
Inter-organ signalling by HRG-7 promotes systemic haem homeostasis.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging.
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Aging is associated with major nuclear changes affecting genomic integrity and gene expression. Here we compare the gene expression profiles in the neocortex of young (5 months old) and old (30 months old) B6xC3 F1 mice.
Publication Title
SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging.
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus
- 30 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Metformin, a commonly used drug prescribed to treat type-2 diabetes, has been found to extend health span and delay cancer incidence and progression. Here, we report that starting chronic treatment with low dose of metformin (0.1% w/w in diet) at one year of age extends health and lifespan in male mice, while a higher dose (1% w/w) was toxic. Treatment with low dose metformin mimicked some of the benefits of calorie restriction, such as improved physical performance, increased insulin sensitivity, and reduced LDL and cholesterol levels. At a molecular level, metformin increased AMP-activated protein kinase activity without attenuation of the mitochondrial electron transport chain activities. Metformin treatment resulted in lower chronic inflammation and increased antioxidant protection, suggesting that the ability of metformin to improve health of laboratory animals may stem from these factors. Our results support that metformin supplementation could be beneficial in extending health and lifespan in humans.
Publication Title
Metformin improves healthspan and lifespan in mice.
Sample Metadata Fields
Sex, Specimen part
View Samples