Filters
Technology
Platform
Homo sapiens
3 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Absent in Melanoma 2 (AIM2) is a member of the HIN-200 family of hematopoietic, IFN-inducible nuclear proteins associated with infection defense and tumor pathology. Recently, AIM2 was found to act as a DNA sensor in innate immunity. In addition, a high frequency of AIM2-alterations was observed in microsatellite unstable tumors. To elucidate AIM2 function in colorectal tumors, we here addressed AIM2-responsive genes by microarray. Among genes up-regulated by AIM2, there were a number of interferon-stimulated genes (ISGs: IFIT1, IFIT2, IFIT3, IFI6, IRF7, ISG15, HLA-DRA, HLA-DRB, TLR3 and CIITA) as well as genes involved in intercellular adhesion and matrix remodeling. Expression of ISGs correlated with expression of AIM2 in ten different IFN- treated colorectal cancer cell lines. Moreover, knock-down of AIM2 resulted in reduced expression of HLA-DRA, HLA-DRB, and CIITA in IFN- treated cells. IFN- independent induction of HLA-DR genes and their encoded proteins was also demonstrated upon transient induction of AIM2. STAT-signaling was not involved in IFN- independent induction of ISGs, arguing against participation of cytokines released in an autocrine manner. Our data indicate that AIM2 mediates IFN- dependent and independent induction of several Interferon stimulated genes (ISGs) including genes encoding the MHC II antigens HLA-DR and .
Publication Title
Absent in Melanoma 2 (AIM2) is an important mediator of interferon-dependent and -independent HLA-DRA and HLA-DRB gene expression in colorectal cancers.
Sample Metadata Fields
Cell line
View Samples- Sus scrofa
- 1 Downloadable Sample
Illumina HiSeq 2000
Description
So far, the majority of research on piRNAs was carried out in popular model organisms such as fruit fly and mouse, which however do not closely reflect human PIWI biology. Thus, we high-throughput sequenced and computationally analyzed piRNAs expressed in the adult testis of the pig owing to its full set of mammalian Piwi paralogs, availability for repeat experiments and the existence of elementary data from previous studies on the porcine PIWI/piRNA system. We provide an exhaustive characterization of porcine piRNAs and genomic piRNA clusters. In addition, we reveal that a considerable proportion of piRNAs matches protein coding genes, exhibiting characteristics that point to a biogenesis within the post-transcriptional silencing mechanism of the PIWI/piRNA pathway, commonly referred to as ping pong cycle. We further show that the majority of identified piRNA clusters spans exonic sequences of protein-coding genes or pseudogenes, which indicates the existence of different mechanisms for the generation of piRNAs directed against mRNA. Our data provides evidence that spliced mRNAs, derived from such loci, are not only targeted by piRNAs but are also subject to ping pong cycle processing. Finally, we demonstrate that homologous genes are targeted by piRNAs in pig, mouse and human. Altogether, this strongly suggests a role for mammalian piRNA clusters in gene regulation alongside of TE repression.
Publication Title
piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
15-20 cm tall 35S::Myc-GR-bdl plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes Overall design: RNA from three samples was pooled and analyzed by RNAseq.
Publication Title
Spatial specificity of auxin responses coordinates wood formation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
15-20 cm tall PXY:GR-MP?III/IV plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes Overall design: RNA from three samples was pooled and analyzed by RNAseq.
Publication Title
Spatial specificity of auxin responses coordinates wood formation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
ALS is a uniformly fatal neurodegenerative disease in which motor neurons in the spinal cord and brain stem are selectively lost. Individual motor - groups of motor neurons innervating single muscles - show widely varying degrees of disease resistance: in the final stages of ALS, nearly all voluntary movement is lost but eye movement and eliminative and sexual functions remain relatively unimpaired. These functions are controlled by motor neurons of the oculomotor (III), trochlear (IV) and abducens (VI) nuclei in the midbrain and brainstem, and by Onufs nucleus in the lumbosacral spinal cord, respectively. Correspondingly, in ALS autopsies the oculomotor and Onufs nuclei are almost completely preserved. We used microarray profiling of isolated wildtype mouse motor neurons to identify genes whose expression was characteristic of both oculomotor and Onufs nuclei but not of vulnerable lumbar spinal neurons, or vice versa.
Publication Title
Neuronal matrix metalloproteinase-9 is a determinant of selective neurodegeneration.
Sample Metadata Fields
Sex, Specimen part
View Samples
GSE24558- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Glioblastoma stem-like cells give rise to tumour endothelium.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Transcriptome analysis of RNAs from brain tumor
Publication Title
Glioblastoma stem-like cells give rise to tumour endothelium.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
GBM is a heterogenous brain tumor with hyperproliferation of endothelial cells. In order to understand the cellular mechanism of vasculogenesis in GBM, four fractions of cells are seperated. Microarray assays was performed to examine the potential lineage relationship and the signal pathways involved in determining the cell identity and function.
Publication Title
Glioblastoma stem-like cells give rise to tumour endothelium.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Rattus norvegicus
- 75 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Demonstration of reduced biological effects with a prototypic modified risk tobacco product.
Publication Title
A 28-day rat inhalation study with an integrated molecular toxicology endpoint demonstrates reduced exposure effects for a prototypic modified risk tobacco product compared with conventional cigarettes.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Homo sapiens
- 132 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
A cross sectional study using data collected at the time of liver biopsy, the final eligibility assessment for participation in iWITH (NCT01638559), an immunosuppression withdrawal trial.
Publication Title
Evidence of Chronic Allograft Injury in Liver Biopsies From Long-term Pediatric Recipients of Liver Transplants.
Sample Metadata Fields
Specimen part
View Samples