Filters
Technology
Platform
Saccharomyces cerevisiae
15 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose.
Publication Title
Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Analysis of human primary macrophages after live Lactobacillus rhamnosus GG (LGG) or LC705 stimulation for 6h and 24h. The results reveal novel mechanisms for probiotics-induced activation of the healthy human innate immune system.
Publication Title
Nonpathogenic Lactobacillus rhamnosus activates the inflammasome and antiviral responses in human macrophages.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 10 Downloadable Samples
Illumina HiSeq 2000
Description
Cell lines derived from NK cell neoplasms were characterized using RNA sequencing and high-throughput drug sensitivity profiling to identify therapeutically actionable drivers in malignant NK cells. Overall design: RNA sequencing data was obtained from natural killer and T cell lines for gene expression profiling and mutation detection in parallel with drug sensitivity profiling. The ''NK_cell_line_GEO_drug_sensitivity.txt'' contains drug sensitivity scores of cell lines screened using 459 compounds. Breifly, compounds were preprinted on 384-well plates (Corning) in five different concentrations covering a 10,000-fold concentration range with an acoustic liquid handling device (Echo 550, Labcyte Inc.) and dissolved in 5 l culture medium on a shaker for 10 min. 20 l of single-cell suspension of cell lines (3,000 cells per well) were dispensed using Multi-Drop Combi peristaltic dispenser (Thermo Scientific). Plates were incubated at 37 C and 5% CO2 for 72 h after which cell viability was measured using CellTiter-Glo 2.0 reagent (Promega) according to the manufacturer s instructions with a Pherastar FS plate reader (BMG Labtech). Cell viability luminescence data were normalized to DMSO-only wells (negative control) and 100 mM benzethonium chloride-containing wells (positive control). The data were quantified using the drug sensitivity score (DSS) (Yadav et al., Scientific Reports 2014).
Publication Title
Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 23 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
Metazoans utilize a handful of highly conserved signaling pathways to create a signaling backbone that governs all stages of development, by providing spatial and temporal cues that influence gene expression. How these few signals have such a versatile developmental action is of significance to evolution, development, and disease. Their versatility likely depends upon the larger-scale network they form through integration. Such integration is exemplified by cross-talk between the Notch and the Receptor Tyrosine Kinase (RTK) pathways. We examined the transcriptional output of Notch-RTK cross-talk during Drosophila development and present in vivo data that supports a role for selected mutually-regulated genes as potentially important nodal points for signal integration. We find the complex interplay between these pathways involves their mutual regulation of numerous core components of RTK signaling in addition to targets that include components of all the major signalling pathways (TGF-, Hh, Jak/Stat, Nuclear Receptor and Wnt). Interestingly, Notch-RTK integration did not lead to general antagonism of either pathway, as is commonly believed. Instead, integration had a combinatorial effect on specific cross-regulated targets, which unexpectedly included the majority of Ras-responsive genes, suggesting Notch can specify the response to Ras activation.
Publication Title
Nodal points and complexity of Notch-Ras signal integration.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Ubiquitin Ligase (UBE4B) and Lysine-Specific Demethylase (LSD1) are post-translational modifying enzymes affecting lysine ubiquitination and methylation of several important regulatory proteins, and are synergisticaly important for protein quality control. To inwestigate their role in cell signaling, we analyzed global mRNA levels in HEK293T cells that were knocked down with shRNAs against UBE4B, LSD1, both UBE4B and LSD1, and non-targeting control (CTRL).
Publication Title
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
Sample Metadata Fields
Cell line, Time
View Samples
GSE99561- Mus musculus, Unidentified
- 267 Downloadable Samples
- Illumina HiSeq 2000, Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Systems genetics identifies a co-regulated module of liver microRNAs associated with plasma LDL cholesterol in murine diet-induced dyslipidemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus, Unidentified
- 267 Downloadable Samples
Affymetrix Mouse Gene 2.1 ST Array (mogene21st), Illumina HiSeq 2000
Description
Genetic variation, in addition to environmental influences like diet, can govern the expression levels of microRNAs (miRNAs). MiRNAs are commonly found to operate cooperatively in groups to regulate gene expression. To investigate this, we combined small RNA sequencing, clinical phenotypes, and microarray data measuring gene expression from an outbred mouse model, the Diversity Outbred population. In the DO population, each individual has a distinct genome that is a mosaic of 8 inbred founder strains. We used these data to identify co-regulated modules of miRNAs and genes that are influenced by genetics and diet, and identify relationships between the modules and phenotypes in over 200 DO mice.
Publication Title
Systems genetics identifies a co-regulated module of liver microRNAs associated with plasma LDL cholesterol in murine diet-induced dyslipidemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Approximately, KSHV vIRF4 deregulate 284 genes by two-folds
Publication Title
Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 (vIRF4) targets expression of cellular IRF4 and the Myc gene to facilitate lytic replication.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Phosphatidylcholine transfer protein (PC-TP, a.k.a StarD2) is abundantly expressed in liver and is regulated by PPAR. When fed the synthetic PPAR ligand fenofibrate, Pctp-/- mice exhibited altered lipid and glucose homeostasis. Microarray profiling of liver from fenofibrate fed wild type and Pctp-/- mice revealed differential expression of a broad array of metabolic genes, as well as their regulatory transcription factors. Because its expression controlled the transcriptional activities of both PPAR and HNF4 in cell culture, the broader impact of PC-TP on nutrient metabolism is most likely secondary to its role in fatty acid metabolism.
Publication Title
Regulatory role for phosphatidylcholine transfer protein/StarD2 in the metabolic response to peroxisome proliferator activated receptor alpha (PPARalpha).
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The rate of cell differentiation is tightly controlled and critical for normal development and stem cell differentiation. However, so far it has been difficult to control the rate of ESCs differentiation. Here we report the acceleration of the differentiation rate due to the activation of protein kinase A (PKA) and the associated early loss of embryonic stem cells (ESCs) pluripotency markers and the early appearance of mesodermal and other germ layer cell markers.
Publication Title
Protein kinase A accelerates the rate of early stage differentiation of pluripotent stem cells.
Sample Metadata Fields
Time
View Samples