We undertook an inter-laboratory effort to generate high-quality quantitative data for a very large number of cellular components in yeast using transcriptome and metabolome analysis. We ensured the high-quality of the experimental data by evaluating a wide range of sampling and measurement techniques. The data were generated for two different yeast strains, each growing under two different growth conditions and based on integrated analysis of the high-throughput data we hypothesize that differences in growth rates and yields on glucose between the two strains are due to differences in protein metabolism.
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.
No sample metadata fields
View SamplesThe functional shift of quiescent endothelial cells into tip cells that migrate and stalk cells that proliferate is a key event during sprouting angiogenesis. We previously showed that the sialomucin CD34 is expressed in a small subset of cultured endothelial cells and that these cells extend filopodia: a hallmark of tip cells in vivo. In the present study, we characterized endothelial cells expressing CD34 in endothelial monolayers in vitro. We found that CD34-positive human umbilical vein endothelial cells show low proliferation activity and increased mRNA expression of all known tip cell markers, as compared to CD34- negative cells. Genome-wide mRNA profiling analysis of CD34-positive endothelial cells demonstrated enrichment for biological functions related to angiogenesis and migration, whereas CD34-negative cells were enriched for functions related to proliferation. In addition, we found an increase or decrease of CD34-positive cells in vitro upon exposure to stimuli that enhance or limit the number of tip cells in vivo, respectively. Our findings suggest cells with virtually all known properties of tip cells are present in vascular endothelial cell cultures and that they can be isolated based on expression of CD34. This novel strategy may open alternative avenues for future studies of molecular processes and functions in tip cells in angiogenesis.
CD34 marks angiogenic tip cells in human vascular endothelial cell cultures.
Specimen part, Subject
View SamplesArabipdosis thaliana (ecotype Col-0) was infected with the root pathogen Plasmodiophora brassicae. Gene expression of the host plant has been analyzed at two time points after inoculation (10 and 23 days after inoculation) compared to the correspondend control plants.
Transcriptome analysis of Arabidopsis clubroots indicate a key role for cytokinins in disease development.
Age, Specimen part, Cell line, Time
View SamplesHuman embryonic stem cells were differentiated into peripheral sensory neurons via the intermediate generation of neural crest like cell (NCC). Using various markers we identified these cells as LTMR. We then analyzed there complete transcriptional profile in comparison to the intermediate neural crest like cells. Overall design: mRNA expression data of human ESC-derived sensory neuron clusters (10-20 cells) and human ESC-derived neural crest like cells (~100 cells) was generated by illumina deep sequencing
PIEZO2 is required for mechanotransduction in human stem cell-derived touch receptors.
No sample metadata fields
View SamplesLeaf transcriptome comparison of untransformed Col-0 Arabidopsis plants with plants transformed to be anti-sense for AtAOX1a (alternative oxidase). Two bio-replicates were sampled, for a total of four microarray chipsCol-0 and anti-sense leaf tissue from a first planting (samples GSM45208 and GSM45231, respectively), and from a second planting made one week later (samples GSM45209 and GSM45278, respectively). See sample descriptions for growth conditions and microarray procedure.
Characterization of transformed Arabidopsis with altered alternative oxidase levels and analysis of effects on reactive oxygen species in tissue.
No sample metadata fields
View SamplesCell Line: This experiment was designed to measure the transcriptional responses to four kinase inhibitors across a five-logarithm dose range. The A549 human lung cancer cell line was treated with dasatinib, imatinib or nilotinib (4 hours and 20 hours) or PD0325901 (4 hours). Treatments used a 12-point dose range (30 uM with 3-fold dilutions down to 0.17 nM; 0.5% DMSO vehicle for all treatments). Experimental design prevented row or column handling effects being confounded with dose effect.
Transcriptional profiling of the dose response: a more powerful approach for characterizing drug activities.
Disease, Cell line, Compound, Time
View SamplesIdentify genes involved in regulation of inflammatory responses and gene-environemnt interactions, in macrophages from a set of mouse inbred strains termed the HMDP. The HMDP is a genetically diverse mapping panel comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010.
Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages.
Sex, Age, Specimen part
View SamplesMurine healthy tissue samples, DCIS and invasive mammary tumors were analyzed in order to identify marker genes which show enhanced expresssion in DCIS and invasive ductal carcinomas.
Identification of early molecular markers for breast cancer.
Specimen part
View SamplesHuman healthy tissue samples, DCIS and invasive mammary tumors were analyzed in order to identify marker genes which show enhanced expresssion in DCIS and invasive ductal carcinomas.
Identification of early molecular markers for breast cancer.
Specimen part, Disease, Disease stage
View SamplesDifferencies between groups between pre and post haematopoietic stem cell transplantation children
Genetic Background of Immune Complications after Allogeneic Hematopoietic Stem Cell Transplantation in Children.
Specimen part, Disease stage
View Samples