To search for rapid changes in gene expression following BCR activation, we performed DNA microarray analysis of activated splenic B cells with and without anti-IgM treatment for 3 hour. The expression of a remarkably large set of genes differed significantly.
Initiation of antigen receptor-dependent differentiation into plasma cells by calmodulin inhibition of E2A.
Age, Specimen part
View SamplesRNA-Seq technique was applied to investigate the effects of four cDNA amplification kits and two RNA-Seq library preparation kits to the deep sequencing results at different perspectives. Overall design: The same set of semen samples were applied to investigate the qualitative and quantitative effect of four cDNA amplification methods and two RNA-Seq library preparation methods on sperm transcript profiling.
A comparison of sperm RNA-seq methods.
No sample metadata fields
View SamplesRNA-Seq technique was applied to investigate the effects of two semen collection methods (Pelleted vs Liquefied) and two sperm purification methods (SCLB vs PS) to the integrity of isolated RNAs at different perspectives. Overall design: The same set of semen samples were applied to investigate the qualitative and quantitative effect of semen collection methods and sperm cell purification methods on sperm transcript profiling.
Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling.
Subject
View SamplesThe autoregulation of mycorrhization (AOM) describes a plant regulatory mechanism that limits the number of infection events by arbuscular mycorrhizal fungi. The key signal mediator is a receptor kinase (GmNARK) that acts in the shoots. Early signals of the mycorrhizal symbiosis induce a root-derived signal that activates GmNARK in the shoot finally leading to a systemic repression of subsequent infections in the root. So far, less is known about the signals down-stream of GmNARK. To find genes regulated by GmNARK in a mycorrhiza-dependent as well as in a mycorrhiza-independent manner, we used the Affymetrix GeneChip for soybean. In general, mycorrhizal root systems consist of both colonized and non-colonized, but autoregulated roots. To physically separate those two root types for transcript analysis of specifically regulated genes, we used the split-root system. Transcript profiling during AOM was done with material of Bragg wild-type and of the nark mutant nts1007, either non-inoculated or partially inoculated with the mycorrhizal fungus Rhizophagus irregularis (formerly Glomus intraradices). Wild-type and nark mutants were inoculated with R. irregularis on one half of the root-systems (root-parts "A") only. The remaining half of the root-systems stayed non-infected (root-parts "B"). Corresponding controls stayed completely non-infected. Gene expression was analyzed in inoculated root-parts, non-inoculated root-parts and shoots of three individual plants per treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Sara Schaarschmidt. The equivalent experiment is GM53 at PLEXdb.]
Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization.
Age, Specimen part
View SamplesAlthough mast cells elicit proinflammatory and type I IFN responses upon VSV infection, in response to L.monocytogenes (L.m) or S. Typhimurium (S.t), such cells elicit a transcriptional program devoid of type I IFN response.
Mast cells elicit proinflammatory but not type I interferon responses upon activation of TLRs by bacteria.
Specimen part
View SamplesInterferons have been ascribed to mediate antitumor effects. IRF-1 is a major target gene of interferons. It inhibits cell proliferation and oncogenic transformation. Here we show that 60% of all mRNAs deregulated by oncogenic transformation mediated by c-myc and H-ras are reverted to the expression levels of non-transformed cells by IRF-1. These include cell cycle regulating genes. Activation of IRF-1 decreases cyclin D1 expression and CDK4 kinase activity concomitant with dephosphorylation of pRb. These effects of IRF-1 are mediated by inhibition of the MEK-ERK pathway and a transcriptional repression of cyclin D1. IRF-1 mediated effects on cell cycle progression were found to be overridden by ectopic expression of cyclin D1. Ablation of cyclin D1 by RNA interference experiments prevents transformation and tumor growth in nude mice. The data demonstrate that cyclin D1 is a key target for IRF-1 mediated tumor suppressive effects.
Tumor suppression by IFN regulatory factor-1 is mediated by transcriptional down-regulation of cyclin D1.
Specimen part
View SamplesWe report on abundance and transcript profile characteristics of sperm RNAs. Overall design: Examination of RNA population and distribution in spermatozoa
Stability, delivery and functions of human sperm RNAs at fertilization.
Specimen part, Subject
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Activity-dependent regulation of inhibitory synapse development by Npas4.
No sample metadata fields
View SamplesDoxorubicin is considered one of the most potent established chemotherapeutics in the treatment of liposarcoma; however, the response rates usually below 30%, are still disappointing. This study was performed to identify gene expression changes in liposarcoma after doxorubicin treatment. Cells of 19 primary human liposarcoma were harvested intraoperatively and brought into cell culture. Cells were incubated with doxorubicin for 24 h, RNA was isolated and differential gene expression was analysed by the microarray technique.
Heterogeneous in vitro effects of doxorubicin on gene expression in primary human liposarcoma cultures.
Sex
View SamplesFriedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disease usually caused by large homozygous expansions of GAA repeat sequences in intron 1 of the frataxin (FXN) gene. FRDA patients have low FXN mRNA and frataxin protein levels when compared with heterozygous carriers or healthy controls. Presently, there is no effective treatment for FRDA, and biomarkers to measure therapeutic trial outcomes and/or to gauge disease progression are lacking. Peripheral tissues, including blood cells, buccal cells, and skin fibroblasts, can readily be isolated from FRDA patients and used to define molecular hallmarks of disease pathogenesis. However, because these tissues are not directly involved in disease pathogenesis, their relevance as models of the molecular aspects of the disease is yet to be decided. Transcriptome profiling of FRDA skin fibroblasts revealed significantly upregulated expression of genes encoding plasma membrane solute carrier proteins. Conversely, the expression of genes encoding accessory factors and enzymes involved in cytoplasmic and mitochondrial protein synthesis was consistently decreased in the FRDA cells. Finally, comparison of genes differentially expressed in FRDA fibroblasts to 3 previously published gene expression signatures defined for FRDA blood cells showed substantial overlap between the independent datasets, including correspondingly deficient expression of antioxidant defense genes. Together, these results indicate that gene expression profiling of cells derived from peripheral tissues can, in fact, consistently reveal novel molecular pathways of the disease. Overall design: We used RNA sequencing to profile the transcriptomes of primary fibroblast cell lines derived from 18 FRDA patients and 17 unaffected control individuals.
A Comprehensive Transcriptome Analysis Identifies FXN and BDNF as Novel Targets of miRNAs in Friedreich's Ataxia Patients.
Specimen part, Subject
View Samples