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GSE12348
Homo sapiens
9 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
The primary goal of this study was to assess differences in gene expression between prostate cancer cell lines and normal prostate epithelial and stromal cells in primary culture.
Publication Title
DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Microarray experiments were carried out to ascertain whether TOP2 is required for DHT induced androgen receptor target gene expression. We investigated the effect of pharmacological inhibition or RNA interference-mediated depletion of TOP2 on gene expression in androgen-dependent LNCaP prostate cancer cells.
Publication Title
Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Lymphatic valves are specialized units regularly distributed along collecting vessels that allow unidirectional forward propulsion of the lymph, and its efficient transport from tissues to the bloodstream. Lymphatic endothelial cells that cover lymphatic valve sinuses are subjected to complex flow patterns, due to recirculation of the lymph during the collecting vessel pumping cycle. They also express high levels of FOXC2 transcription factor.
Publication Title
FOXC2 and fluid shear stress stabilize postnatal lymphatic vasculature.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Oryza sativa indica group
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Background In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed at progressive stages of development by using microarray and sequence by synthesis technologies to identify genes that regulate anther development. Here we have carried out a comprehensive analysis of rice anther transcriptomes at four distinct stages of development with a focus to identify regulatory components contributing to male meiosis and germline development. Further, these transcriptomes have been compared with transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. Results - To understand the molecular processes that lead to male gametophyte development, transcriptome profiling of four stages of anther development in rice [pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA)] was conducted. Around 22,000 genes were found to be expressed in at least one of the anther developmental stages, with the highest number in MA (18,090) and lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of1,000 genes that are specifically expressed in anther stages. Of them the expression of 453 genes was found to be specific to TPA, whereas 78 and 184 genes were expressed specifically in MA and SCP. Gene ontology and pathway analysis of specifically expressed genes revealed that transcription factors and protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. Conclusions - These data not only provide the transcriptome constituents of four landmark stages of anther development but also identify genes that express exclusively in these stages and therefore may contribute to specific aspects of anther and/or male gametophyte development in rice. Moreover, these gene sets assist in building a deeper understanding of underlying regulatory networks and in selecting candidates for gene function validation.
Publication Title
Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
DOT1L as methyltransferase of H3K79 is implicated in brian development. Here, we further defined DOT1L function in gene expression during cerebellar development using Microarrays. For that we generated Dot1l knockout mice using a Atoh-Cre driver line resulting in a Dot1l knockout within the cerebellum. The RNA of cerebellar tissue of the Dot1l knockout animals was thereby compared to controls. Additionally we compared the RNA levels of cultured CGNP and CGN samples treated with a DOT1L inhibitor versus DMSO treated cells. The data sets reveals potential new gene expression targets of DOT1L in vivo and in vitro, which ensure a correct development of the cerebellum.
Publication Title
Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 30 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Analysis of gene expression change induced by myeloma cells in pDCs. The hypothesis tested in the present study was that myeloma cells inhibit pDCs function by direct contact. Results provide important information of gene expression change in the cocultured of pDCs and myeloma, such as IFNs and IFN regulatory genes, TLR9 signaling pathways.
Publication Title
E-cadherin expression on multiple myeloma cells activates tumor-promoting properties in plasmacytoid DCs.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 20 Downloadable Samples
- Affymetrix Rat Gene 1.1 ST Array (ragene11st)
Description
Identify differentially expressed genes related to the neurodegenerative process in a new animal model of hepatic encephalopathy (HE).
Publication Title
Cerebellar neurodegeneration in a new rat model of episodic hepatic encephalopathy.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 22 Downloadable Samples
Illumina HiSeq 2500, Illumina HiSeq 2000
Description
CD4+ T cells optimize the cytotoxic T cell (CTL) response in magnitude and quality, by unknown molecular mechanisms. We here present the transcriptomic changes, resulting from CD4+ T-cell help during priming, as apparent in effector CTLs. This gene expression signature reveals that CD4+ T-cell help optimizes CTLs in the expression of cytotoxic effector molecules, but also in many other functions that ensure optimal efficacy of CTLs throughout their life cycle. Overall design: Whole transcriptome analysis of effector CD8 T cells primed in the presence or absence of CD4 T cell help after vaccination or virus infection, or treated with agonistic CD27 or blocking CD70 antibody after vaccination.
Publication Title
CD4<sup>+</sup> T Cell Help Confers a Cytotoxic T Cell Effector Program Including Coinhibitory Receptor Downregulation and Increased Tissue Invasiveness.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Protein C (PC) deficiency increases the risk of venous thrombosis (VT) among members of Kindred Vermont II, but fails to fully account for the inheritance pattern. A genome scan of the pedigree supported the presence of a prothrombotic gene on chromosome 11q23 with weaker support on chromosomes 10p12 and 18p11.2-q11.
Publication Title
Cell adhesion molecule 1: a novel risk factor for venous thrombosis.
Sample Metadata Fields
Sex, Age, Specimen part, Race
View Samples