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Comparative 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 13 sets of two color arrays were performed and each individual array included a target sample and a control sample.

ORGANISM(S): Homo sapiens

SUBMITTER: Daisuke Okuzaki

PROVIDER: E-GEOD-16945 | 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

Similar Datasets

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

Focused 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 14 sets of one color arrays were performed. Four technical replicates were performed for each sample.

2010-11-10 | E-GEOD-18247 | biostudies-arrayexpress

Nucleoredoxin is required for the maintenance of Wnt/Î²-catenin signaling in mice embryo

Project description:We previously showed that nucleoredoxin (NRX) suppresses Wnt/Î²-catenin signaling through its binding to Dishevelled (Dvl) (Nat Cell Biol 8, 501-508 (2006)). To clarify the in vivo role of NRX in mammals, we here generate NRX gene-knockout mice (NRX-/- mice) by homologous recombination. NRX-/- mice die around birth. Therefore, we performed microarray analyses with NRX+/+ and NRX-/- embryos of E9.5 and E11.5 stages. Surprisingly, in the genes commonly upregulated at both stages, we could not observe Wnt/Î²-catenin targets. Rather, several target genes for Wnt/Î²-catenin pathway, such as Frizzled2 and Occludin, are downregulated in NRX-/- whole embryos. Frizzled2 is a gene reportedly expressed in developmental heart. Indeed, by RT-PCR analyses we confirmed that the expression of Frizzled2, as well as other Wnt/Î²-catenin target genes, was downregulated in embryonic heart of NRX-/- mice. We also found that the amount of unphosphorylated (i.e. activated) form of Î²-catenin was downregulated in NRX-/- embryonic heart. These results reveal that NRX plays another role which was unidentified in culture cell studies; it is required for the maintenance of Wnt/Î²-catenin signaling activity. Total RNAs were extracted from E9.5 and E11.5 embryos derived from NRX+/+ and NRX-/- C57BL/6J mice using RNeasy extraction kit (Qiagen). Two dye-swapped experiments were performed by hybridizing complimentary RNA (cRNA) labeled with either Cyanine (Cy) -3 or Cy-5 (Perkin-Elmer) onto Whole Mouse Genome Oligo Microarray (G4122A; Agilent Technologies). The signature genes with mean fold changes > +2.0 or < -2.0 at both stages were subjected for further evaluation.

2010-10-26 | E-GEOD-21954 | biostudies-arrayexpress

Expression profiling in primary embryonic fibroblasts deficient for the N-terminal truncation of Lats1

Project description:Lats1 and Lats2 are the mediators of the Hippo pathway that regulates tissue growth and proliferation. Lats1 and Lats2 kinases share 85% sequence identity in the kinase domain. However, their non-kinase regions at the N-terminus are distinct except for Lats conserved domain 1 (LCD1) and LCD2, suggesting that their N-terminal regions are important for Lats1/2-specific functions. In this study, we generated Lats1 knockout mice disrupting the N-terminal region containing LCD1 (Lats1M-NM-^TN/M-NM-^TN). We show that some Lats1M-NM-^TN/M-NM-^TN mice were born safely and grew normally. However, mouse embryonic fibroblasts (MEFs) from Lats1M-NM-^TN/M-NM-^TN mice displayed drastic defects in mitosis, showing enhanced centrosome overduplication, chromosomal misalignment, multipolar spindle formation, chromosome bridging, and cytokinesis failure. Moreover, they displayed accelerated cell cycle and cell growth bypassing a cell-cell contact inhibition like tumor cells, and exhibited anchorage independent growth. Indeed, Lats1M-NM-^TN/M-NM-^TN MEFs produced tumors in nude mice after subcutaneous injection, although the tumor growth rate was much slower than ordinary cancer cells. Furthermore, Yap, the key transcriptional co-activator in the Hippo pathway, was overexpressed and retained stable in Lats1M-NM-^TN/M-NM-^TN MEFs under high cell density, and expression of Lats2 mRNA were down-regulated. Total RNAs were extracted from MEFs under high or low cell density using miRNeasy extraction kit (Qiagen). A Dye-swapped experiment was performed by hybridizing complimentary RNA (cRNA) labeled with either Cyanine (Cy) -3 or Cy-5 (Perkin-Elmer) onto Whole Mouse Genome Oligo Microarray (G4122F; Agilent Technologies). Co-hybridizations were performed and data from Cy3 or Cy5 channels were analyzed as normalized signal intensities rather than as log ratios corresponding to each array.

2012-12-17 | E-GEOD-37871 | biostudies-arrayexpress

Gene expression in mouse leukocytes after CAWS administration

Project description:We performed DNA microarray analyses and compared the difference in the transcriptome between B6 and DBA/2 mice with modest or dramatic sensitivity to CAWS-vasculitis, respectively. Candida albicans water-soluble fraction (CAWS), a mannoprotein-M-NM-2-glucan complex obtained from the culture supernatant of C. albicans NBRC1385, causes CAWS mediated vasculitis (CAWS-vasculitis) with distinct sensitivity among mouse strains. The mouse leukocyte derived from B6 and DBA/2 mice after 2-, 4-, 8-, 9- weeks administration were examined. Each mice was run in singlete or duplicate. Microarray analyses were performed as single-color hybridizations.

2013-09-30 | E-GEOD-44803 | biostudies-arrayexpress

Enhanced expression of Ficolin 1 is a specific gene marker of Takayasu's vasculitis

Project description:Takayasu's arteritis (TA) Vasculitis (angiitis) is a chronic inflammatory disease involving large blood vessels. We here identify the genes whose mRNA levels are commonly augmented in the peripheral blood mononuclear cells (PBMCs) from TA patients regardless of the patient's symptom, active or inactive phase, compared with those of normal volunteers. Among them, ficolin 1 (FCN1) was notable because its mRNA level was more than 4.0 fold in all 8 patients examined. A total of 8 two color arrays were performed and each individual array included a target sample and a control sample.

2012-03-26 | E-GEOD-33910 | biostudies-arrayexpress

Gene expression analysis between CD20- CD138- and CD20+ CD138+ subpopulations using sorted MWCL-1

Project description:For the complete cure of tumors, it is essential to eliminate cancer-initiating cells (CICs). Immunohistochemically, most tumor cells were CD20 and/or CD138 positive in clinical samples of lymphoplasmacytic lymphoma (LPL), and CD20- CD138- cells were hardly detected. Therefore, useful positive markers expressing in a candidate of CICs of LPL are necessary. First, we performed gene expression microarray analysis between CD20- CD138- and CD20+ CD138+ subpopulations using sorted Waldenstrom macroglobulinemia cell line (MWCL-1). Two dye-swap experiment was performed onto Human GE 4Ã44K V2 arrays (G4845A; Agilent Technologies).

2016-02-17 | E-GEOD-73756 | biostudies-arrayexpress

Transcriptome profiling of Lats2 deficient mouse embryonic fibroblasts

Project description:Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. LATS2 depletion dependent dysregulation of PRC2 also effects H3K4me3 and forms negative feedback loop for maintenance of PRC2. Further analyses reveal that LATS2 on chromatin binds to EZH2 and LATS2 has ability to phosphorylate PRC2 in vitro. These LATS2 dependent H3K27me3 targets are highly induced during neurogenesis, and statistical analysis of glioblastoma multiforme reveals that LATS2-high cases show more dedifferentiated transcriptome and poor prognosis with silencing of H3K27me3 targets. These observations suggest that LATS2-mediated epigenome coordination is pivotal for development and disease, including cancer. The labeled cRNAs from three pairs of MEFs (Lats2-/- vs Lats2 +/+) from three independent litter were subjected to Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F in dye swap setup, resulting in eight individual microarrays including tehnical replicates.

2016-07-26 | E-GEOD-63536 | biostudies-arrayexpress

Transcriptome profiling of mouse embryonic fibroblasts upon contact inhibition

Project description:Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. LATS2 depletion dependent dysregulation of PRC2 also effects H3K4me3 and forms negative feedback loop for maintenance of PRC2. Further analyses reveal that LATS2 on chromatin binds to EZH2 and LATS2 has ability to phosphorylate PRC2 in vitro. These LATS2 dependent H3K27me3 targets are highly induced during neurogenesis, and statistical analysis of glioblastoma multiforme reveals that LATS2-high cases show more dedifferentiated transcriptome and poor prognosis with silencing of H3K27me3 targets. These observations suggest that LATS2-mediated epigenome coordination is pivotal for development and disease, including cancer. The labeled cRNAs from MEFs in two different culture conditions (low density vs high density culture) were subjected to Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F in dye swap setup, resulting in two individual microarrays.

2016-07-26 | E-GEOD-63535 | biostudies-arrayexpress

Ficolin-1 is upregulated in leukocytes and glomeruli from microscopic polyangiitis patients

Project description:To search for new markers of active lesions that might help better understand the molecular basis of MPA and aid in its diagnosis, DNA microarray analysis was performed with peripheral blood mononuclear cells (PBMCs). A total of 12 sets of two color arrays were performed and each individual array included a target sample and a control sample.

2013-08-18 | E-GEOD-41744 | biostudies-arrayexpress

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