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GSE54626
Mus musculus
21 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The Her-2/Neu-positive mouse breast cancer cell line was serially co-cultured with minced brain, bone marrow, and lung tissue in an intravital microscopy chamber mounted on the dorsal skinfold of nude mice, alternating with growth in vitro. Gene expression analysis was performed on the cells grown in culture after sorting and further growth in vitro. Gene expression under these growth conditions differed in time and according to the co-cultivated organ tissue. This study reveals genes that are expressed by cells as they adapt differentially to various foreign tissue microenvironments, and may represent a paradigm to discover gene expression changes that occur immediately upon extravasation when cancer metastasizes.
Publication Title
Effects of different tissue microenvironments on gene expression in breast cancer cells.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 33 Downloadable Samples
Illumina HiSeq 2000
Description
We sought to more precisely characterize the different alpha-synuclein (aSyn) 3’UTR mRNA species in normal and PD human brain. High-throughput, whole-transcriptome sequencing of the 3’UTR ends of polyadenylated mRNA transcripts (termed pA-RNAseq; see Methods) was performed on a cohort of 17 unaffected and 17 PD cerebral cortical tissue samples. This revealed 5 aSyn 3’UTR isoforms, with lengths of 290, 480, 560, 1070 and 2520 nt. Of these, the 560 nt and 2520 nt forms were predominant. The existence and relative preponderance of these species was further confirmed by Northern Blot. We next hypothesized, that aSyn 3’UTR selection might be altered in PD. Comparison of pA-RNAseq profiles from PD and unaffected cerebral cortex samples revealed an increase in the preponderance of the long 3’UTR species (>560 nt) relative to shorter species (<560 nt). Such a relative increase in aSynL was confirmed by Quantitative real-time RT-PCR (rt-qPCR) and appeared specific for PD, as the increase was also observed by comparison to RNA from amyotrophic lateral sclerosis patient samples. We note that the modified aSyn 3’UTR selection associated with PD patient tissue was detected in cerebral cortex tissue, which typically harbors pathological evidence of the disease process without frank cell loss; thus, this phenotype is unlikely to be a secondary consequence of neurodegeneration. Overall design: Comparison of 3''UTR ends of alpha-synuclein in PD and unaffected brain cortex
Publication Title
Alternative α-synuclein transcript usage as a convergent mechanism in Parkinson's disease pathology.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Comparison of gene expression signatures in hESC-derived gastrointestinal precursors, enterospheres and primary human tissues to determine lineage and cell type identity.
Publication Title
Functional Enterospheres Derived In Vitro from Human Pluripotent Stem Cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 334 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
Based on preliminary data demonstrating that macrophages are critical regulators of Helicobacter pylori colonization and gastric pathology in mice, we sought to investigate how macrophages may serve as bacterial reservoirs of intracellular H. pylori. Overall design: BMDM were isolated from WT and PPARg-/- mice and cultured with M-CSF for 7 days to promote macrophage differentiation. Fully differentiation macrophages were challenged with H. pylori strains SS1 at an MOI of 10 for 15 minutes. Extracellular bacteria was then eliminated by gentamycin treatment. Cells were collected at 0, 60, 120, 240, 360 and 720 minutes post gentamycin treatment to ascertain whole transcriptome differential gene expression during infection.
Publication Title
Identification of new regulatory genes through expression pattern analysis of a global RNA-seq dataset from a Helicobacter pylori co-culture system.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
To analyze the gene expression alteration after stroke, we used Middle Cerebral Artery Occlusion model of rats. By comparing with Sham operated rats, we extracted the mRNAs whose expressions are alterated by stroke.
Publication Title
Gene Expression Analysis of the Effect of Ischemic Infarction in Whole Blood.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 78 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Coordinated regulation of hepatic and adipose tissue transcriptomes by the oral administration of an amino acid mixture simulating the larval saliva of Vespa species.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 42 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
VAAM stands for an amino acid mixture simulating the composition of Vespa, a hornet larval saliva. We conducted a comparative study on metabolism-regulatory roles of VAAM, casein-simulating amino acid mixture (CAAM), and pure water on murine hepatic and adipose tissue transcriptomes. Mice were orally fed VAAM solution ( 0.675 g/ kg BW = 2% of food-derived amino acids = 0.38% of total food energy/ day), CAAM solution ( 0.675 g / kg BW/ day) or water under ad libitum for five days. Hepatic transcriptome comparison of VAAM, CAAM and water-treated groups revealed a VAAM-specific regulation of the metabolic pathway, i.e., the down-regulation of glycolysis and fatty acid oxidation, and up-regulation of poly unsaturated fatty acid synthesis and glycogenic amino acids utilization in TCA cycle. Similar transcriptomic analysis of white and brown adipose tissues (WAT and BAT) suggested the up-regulation of phospholipid synthesis in WAT and the negative regulation of cellular processes in BAT. Because these coordinated regulations of tissue transcriptomes implicated the presence of upstream signaling common to these tissues, we conducted Ingenuity Pathways Analysis of these transcriptomes with the results that estrogenic and glucagon signals seemed to be activated in liver and WAT as well as beta-adrenergic signaling did in the three tissues by administration of VAAM. Our data provide a clue to understanding the role of VAAM in metabolic regulation of multiple tissues.
Publication Title
Coordinated regulation of hepatic and adipose tissue transcriptomes by the oral administration of an amino acid mixture simulating the larval saliva of Vespa species.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 36 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
VAAM stands for an amino acid mixture simulating the composition of Vespa, a hornet larval saliva. We conducted a comparative study on metabolism-regulatory roles of VAAM, casein-simulating amino acid mixture (CAAM), and pure water on murine hepatic and adipose tissue transcriptomes. Mice were orally fed VAAM solution ( 0.675 g/ kg BW = 2% of food-derived amino acids = 0.38% of total food energy/ day), CAAM solution ( 0.675 g / kg BW/ day) or water under ad libitum for five days. Hepatic transcriptome comparison of VAAM, CAAM and water-treated groups revealed a VAAM-specific regulation of the metabolic pathway, i.e., the down-regulation of glycolysis and fatty acid oxidation, and up-regulation of poly unsaturated fatty acid synthesis and glycogenic amino acids utilization in TCA cycle. Similar transcriptomic analysis of white and brown adipose tissues (WAT and BAT) suggested the up-regulation of phospholipid synthesis in WAT and the negative regulation of cellular processes in BAT. Because these coordinated regulations of tissue transcriptomes implicated the presence of upstream signaling common to these tissues, we conducted Ingenuity Pathways Analysis of these transcriptomes with the results that estrogenic and glucagon signals seemed to be activated in liver and WAT as well as beta-adrenergic signaling did in the three tissues by administration of VAAM. Our data provide a clue to understanding the role of VAAM in metabolic regulation of multiple tissues.
Publication Title
Coordinated regulation of hepatic and adipose tissue transcriptomes by the oral administration of an amino acid mixture simulating the larval saliva of Vespa species.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Photobiomodulation (PBM) with blue light induces a biphasic dose response curve in proliferation of immortalized human keratinocytes (HaCaT), with a maximum anti-proliferative effect reached with 30min (41.4J/cm). The aim of this study was to test the photobiomodulatory effect of 41.4J/cm2 blue light irradiation on ROS production, apoptosis and gene expression at different time points after irradiation of HaCaT cells in vitro. ROS concentration was increased 30min after irradiation. However, already 1h after irradiation, cells were able to reduce ROS and balance the concentration to a normal level. The sudden increase in ROS did not damage the cells, which was demonstrated with FACS analysis where HaCaT cells did not show any sign of apoptosis after blue light irradiation. Furthermore, a time course could be seen in gene expression analysis after blue light, with an early response of stimulated genes already 1h after blue light irradiation, leading to the discovery of the aryl hydrocarbon receptor as possible target for blue light irradiation.
Publication Title
Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light.
Sample Metadata Fields
No sample metadata fields
View Samples