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Focused transcription profiling of peripheral blood mononuclear cells from vasculitis patients

ABSTRACT: Peripheral blood mononuclear cells (PBMCs) from 13 vasculitis patients expressed varying gene profiles. A total of 14 sets of one color arrays were performed. Four technical replicates were performed for each sample.

ORGANISM(S): Homo sapiens

SUBMITTER: Daisuke Okuzaki

PROVIDER: E-GEOD-18247 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genopal™: a novel hollow fibre array for focused microarray analysis.

Okuzaki Daisuke D Fukushima Tatsunobu T Tougan Takahiro T Ishii Tomonori T Kobayashi Shigeto S Yoshizaki Kazuyuki K Akita Takashi T Nojima Hiroshi H

DNA research : an international journal for rapid publication of reports on genes and genomes 20101108 6

Expression profiling of target genes in patient blood is a powerful tool for RNA diagnosis. Here, we describe Genopal™, a novel platform ideal for efficient focused microarray analysis. Genopal™, which consists of gel-filled fibres, is advantageous for high-quality mass production via large-scale slicing of the Genopal™ block. We prepared two arrays, infectant and autoimmunity, that provided highly reliable data in terms of repetitive scanning of the same and/or distinct microarrays. Moreover, w ...[more]

PMID: 21059707

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Genopal: a novel platform for focused microarray analysis

Project description:This SuperSeries is composed of the following subset Series: GSE16945: Comparative transcription profiling of peripheral blood mononuclear cells from vasculitis patients GSE18247: Focused transcription profiling of peripheral blood mononuclear cells from vasculitis patients Refer to individual Series

2010-11-10 | E-GEOD-18316 | biostudies-arrayexpress

TLR 4 Signaling Inhibitory Pathway Induced by Green Tea Polyphenol Epigallocatechin-3-Gallate through 67-kDa Laminin Receptor

Project description:Epigallocatechin-3-gallate (EGCG), a major active polyphenol of green tea, has been shown to downregulate inflammatory responses in macrophages; however, the underlying mechanism has not been understood. Recently, we identified the 67-kDa laminin receptor (67LR) as a cell-surface EGCG receptor that mediates the anti-cancer action of EGCG at physiologically relevant concentrations (0.1-1 mM). Here we show the molecular basis for the downregulation of TLR4 signal transduction by EGCG at 1 mM in macrophages. Anti-67LR antibody treatment or RNAi-mediated silencing of 67LR resulted in abrogation of the inhibitory action of EGCG on LPS-induced activation of downstream signaling pathways and target gene expressions. Additionally, we found that EGCG reduced the TLR4 expression through 67LR. Interestingly, EGCG induced a rapid upregulation of Tollip protein, a negative regulator of TLR-signaling, and this EGCG action was prevented by 67LR silencing or anti-67LR antibody treatment. RNAi-mediated silencing of Tollip impaired the TLR4 signaling inhibitory activity of EGCG. Taken together, these findings demonstrate that 67LR plays a critical role in mediating anti-inflammatory action of a physiologically relevant EGCG and Tollip expression could be modulated through 67LR. These results provide a new insight into the understanding of negative regulatory mechanisms for TLR4 signaling pathway and consequent inflammatory responses which are implicated in the development and progression of many chronic diseases. We quantified expression profile of 210 inflammatory-relating genes in the 67LR-downregulated cells treated with LPS or/and EGCG by microarray

2010-04-20 | E-GEOD-21320 | biostudies-arrayexpress

Interferon signaling related gene expression and clinical outcome of chronic hepatitis C

Project description:Chronic hepatitis C (CH) frequently developed liver cirrhosis and hepatocellular carcinoma without suitable treatment. However, peginterferon(IFN) and ribavirin therapy (combination therapy), which is present standard therapy, is imperfect effect because of several side effect. We attempt to catalog IFN related gene expression profile according to the response of combination therapy in to predict the outcome of drug-response before administration and establish the adequate treatment according to the individual clinical information. Chip1 [GPL9960-related Samples]: We quantified expression profile of 200 IFN related genes by microarray in the liver biopsy specimen from 88 CH patients without history of anti-viral therapy, 10 fatty liver patients without HCV infection were also enrolled. Chip2 [GPL9962-related Samples]: We quantified expression profile of 37 IFN related genes by microarray in the liver biopsy specimen from 88 CH patients without history of anti-viral therapy, 10 fatty liver patients without HCV infection were also enrolled.

2010-02-10 | E-GEOD-20119 | biostudies-arrayexpress

Gene Expression Profiles of PBMC Subsets in Acute GVHD Following Cord Blood Transplantation

Project description:This SuperSeries is composed of the following subset Series: GSE10512: Gene Expression Profiles of PBMC Subsets in Acute GVHD Following Cord Blood Transplantation (IMS v.1) GSE10513: Gene Expression Profiles of PBMC Subsets in Acute GVHD Following Cord Blood Transplantation (IMS v.2) Keywords: SuperSeries Refer to individual Series

2008-12-21 | E-GEOD-10572 | biostudies-arrayexpress

Gene Expression Profiles of PBMC Subsets in Acute GVHD Following Cord Blood Transplantation (IMS v.2)

Project description:In comparison with allogeneic hematopoietic stem cell transplantation using other sources, umbilical cord blood transplantation (UCBT) offers substantial clinical advantages including a lower incidence and severity of acute graft-versus-host disease (GVHD) despite the use of allogeneic UCB stem cells with more disparate HLA. However, detailed pathophysiology of acute GVHD developed after UCBT has not yet been clarified. Here, we examined the roles of inflammatory cells in the pathogenesis of acute GVHD following UCBT, by expression profiling of a total of 615 genes in each of 4 subsets (CD4+, CD8+, CD14+, and CD56+) of peripheral blood mononuclear cells (PBMCs), which were taken from 5 patients with hematologic malignancy, in whom acute GVHD had developed after UCBT. By comparing expression profiles measured during acute GVHD with those measured upon discharge (recovery phase), for each subset of PBMCs, we identified immuno-regulatory genes which were assumed to be linked to the pathogenesis of acute GVHD. Keywords: disease state analysis CD4+, CD8+, CD14+, and CD56+ cell subsets were isolated from the peripheral blood mononuclear cells (PBMCs) of 5 patients with hematologic malignancy, in whom acute GVHD had developed after cord blood transplantation. PBMCs were taken twice â during acute GVHD phase and upon discharge (recovery phase), from each patient. By using a custom-made fibrous oligonucleotide DNA microarray Genopal (Mitsubishi Rayon), we compared expression profiles of 615 unique genes measured during acute GVHD with those measured upon discharge (recovery phase), for each subset of PBMCs.

2010-05-15 | E-GEOD-10513 | biostudies-arrayexpress

Association of replication restart proteins with sites of increased transcriptional activity in Bacillus subtilis

Project description:Antibodies against DnaD and DnaB were used to immunoprecipitate genome bound complexes of these proteins in fast growing and slow growing cells as well as in two strains with a constitutively induced Pxis promoter or repressed Pxis promoter. CHIP-chip analysis was then carried out to determine their sites of interaction in vivo. CHI-chip analysis was carried out by Oxford Gene Technology (OGT) wwho also designed and prepared the arrays. Antibodies against DnaD and DnaB were used to immunoprecipitate genome bound complexes of these proteins in fast growing and slow growing cells, as well as in two strains with a constitutively induced Pxis promoter or repressed Pxis promoter. CHIP-chip microarray analysis was carried out by OGT who obtained the raw data. Data were visualized in CHIP Browser provided by OGT.

2010-12-01 | E-GEOD-25736 | biostudies-arrayexpress

Transcriptional dose-response curves for copper for the mussel Mytilus californianus

Project description:Transcriptional dose-response curves for copper for the mussel Mytilus californianus

2011-11-01 | E-MTAB-810 | biostudies-arrayexpress

Comparative transcription profiling of peripheral blood mononuclear cells from vasculitis patients

Project description:Peripheral blood mononuclear cells (PBMCs) from 13 vasculitis patients expressed varying gene profiles. A total of 13 sets of two color arrays were performed and each individual array included a target sample and a control sample.

2010-11-10 | E-GEOD-16945 | biostudies-arrayexpress

Genome-wide identification of RNA polymerase, RpoD, and RpoS binding sites in Klebsiella pneumoniae MGH 78578

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2012-12-31 | E-GEOD-35927 | biostudies-arrayexpress

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip)

Project description:The genome wide ChIP-on-chip analysis to identify the DNA binding sites for the M.tuberculosis sigma factor Rv3286c (SigF) SigF binding sites were determined by microarray analysis of anti-sigF immunoprecipitated DNA from H37Rv(ΔrsbW/sigF)::pmySigF compared to H37Rv(ΔrsbW/sigF)::pMY769 (both cultured with pristinamycin for 3 days). 4 biological replicates were performed.

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