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  • Of the 142 patients enrolled in Study CHRONOS-1, an open-label, single-arm, Phase II study evaluating the efficacy and safety of single-agent copanlisib in patients with relapsed or refractory, indolent B-cell lymphoma (NCT01660451; Part B), 96 archival formalin-fixed paraffin-embedded tumor tissues were collected under relevant consent and available for tumor macro-dissection, mRNA extraction and gene expression profiling using Affymetrix GeneChip Gene ST 1.0 Arrays (AltheaDx, Inc., San Diego, CA, USA). Of these, only 78 samples were with high quality and passed Affymetrix positive versus negative controls AUC ≥ 0.62. Affymetrix CEL files were processed with RMA (R package affy) using a custom CDF from Brainarray (version 20.0.0). 71 patients with indolent non-Hodgkin lymphoma (iNHL), including 54 with follicular lymphoma (FL), had both response data and evaluable gene expression data with high quality array data sets (array positive versus negative controls AUC ≥ 0.62) and were included in this biomarker analysis. In this study, with the exception of subject # 16349B-53, for which expression values were averaged from three equal aliquots that were amplified and scanned on 3 separate days in order to control for day-to-day batch effect, there was only one sample per subject. Affymetrix raw data (CEL files) and the gene expression matrix generated with RMA for the 78 high quality tumor samples are submitted.
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  • The gene activity during human urinary bladder development is largely unknown. Our aim is to provide gene expression data to identify active genes during development and to facilitate future candidate gene identification for bladder malformations. Here, we make the first step to provide RNA-Seq of time-series bladder tissues between week 5 to 10. Fetal lung is used as reference sample.
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  • Mycoplasma species are highly contagious pathogens, and intramammary Mycoplasma infection is a serious issue for the dairy industry. The bovine mammary epithelial cells (bMEC) play an important role for the eradication of pathogens which cause intramammary infection, however the effects of M. bovis for immune response of bMEC have not been fully clarified. We examined the transcription profiling of bMEC on the stimulation with M. bovis for 6h (3 stimuli, 3 control).
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  • Primary intestinal epithelial cells were isolated from the proximal part of the small intestine from either E16.5 foetal tissue or adult tissue and embedded in matrigel for culturing in in advanced F12/DMEM supplemented with EGF, R-spondin and Noggin. RNA was extracted from cultures established from independent animals and subjected to expression profiling.
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  • They aim of the study is to identify targets of Carboxypeptidase E (CPE) as well as signaling cascades that are affected by CPE which are specific for transmitting its anti-migratory effects in glioma cells by overexpressing CPE and using transcriptomics profiling of mRNAs and microRNAs.
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  • The expression level of the 31 genes (ERF-1 (AT4G17500), ERF2 (AT5G47220), ERF5 (AT5G47230), ERF6 (AT4G17490), ERF11 (AT1G28370), ERF8 (AT1G53170), ERF9 (AT5G44210), ERF59 (AT1G06160), ERF98 (AT3G23230), MYB51 (AT1G18570), STZ (AT1G27730), WRKY28 (AT4G18170), WRKY33 (AT2G38470), WRKY15 (AT2G23320), ZAT6 (AT5G04340), WRKY48 (AT5G49520), RAP2.6L (AT5G13330), K11J9.4 (AT5G61590), bHLH (AT2G43140), GATA3 (AT4G34680), GA2OX6 (AT1G02400), GA3OX1 (AT1G15550), GA2OX4 (AT1G47990), GA20OX1 (AT4G25420), EXLB3 (AT2G18660), MPK3 (AT3G45640), RAP2.2 (AT3G14230)) was measured upon mild osmotic stress (25mM mannitol) in the third leaf of wild-type plants during the proliferating (9 days after stratification (DAS)), expanding (15 DAS) and mature (22 DAS) developmental stage. The expanding third leaf (15 DAS) was harvested at a high temporal resolution (20 min, 40 min, 1 h, 2 h, 4 h, 8 h, 12 h, 16 h, 24 h and 48 h), whereas the proliferating and mature leaf tissues were harvested 24h after transfer to control or 25 mM mannitol-containing medium. A detailed expression pattern over time for each gene was generated with the nCounter Nanostring® technology.
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  • We performed a large-scale expression analysis with inducible gain-of-function (GOF) lines which contain a C-terminal fusion protein of the TF of interest and a glucocorticoid receptor (GR) domain, driven by a constitutive 35S promoter. Such fusion proteins reside in the cytosol and can only translocate to the nucleus in the presence of dexamethasone (DEX), enabling the TF to regulate its downstream target genes (Corrado and Karali, 2009). In total 18 GOF lines were used of the following TFs: ERF-1 (AT4G17500), ERF2 (AT5G47220), ERF5 (AT5G47230), ERF6 (AT4G17490), ERF11 (AT1G28370), ERF8 (AT1G53170), ERF9 (AT5G44210), ERF59 (AT1G06160), ERF98 (AT3G23230), MYB51 (AT1G18570), STZ (AT1G27730), WRKY28 (AT4G18170), WRKY33 (AT2G38470), WRKY15 (AT2G23320), ZAT6 (AT5G04340), WRKY48 (AT5G49520), RAP2.6L (AT5G13330) and the control 35S::GFP-GR. To get an indication of which genes are direct or indirect targets of the induced TF, we performed a time-course experiment. All GOF lines were transferred at 15 DAS to DEX-containing medium and the third leaf was harvested at 1 h, 2 h, 4 h, 8 h and 24 h after transfer. The expression of 30 TFs (17 TFs listed above and WRKY6 (AT1G62300), WRKY30 (AT5G24110) and WRKY40 (AT1G80840), GA2OX6 (AT1G02400), GA20OX1 (AT4G25420), ACS6 (AT4G11280), MPK3 (AT3G45640), DEL1 (AT3G48160), UVI4 (AT2G42260), CYCA3;1 (AT5G43080), CYCB1;2 (AT5G06150), XET (AT1G10550), EXPA5 (AT3G29030)) was measured with nCounter Nanostring (Geiss et al, 2008). The time-course experiment gives an indication of whether a gene is putatively a direct, and thus induced during the early time points, or an indirect target of the induced TF.
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  • In order to gain a global temporal picture of epiblast potency across implantation, we collected mouse embryos at E4.5, E4.75 and E5.0, and dissected the epiblast for deep-sequencing analysis.
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  • Myocyte enhancer factor 2 contributes as a transcription factor to cardiac remodeling processes. We wanted to link and compare known myocyte enhancer factor 2 targets to overall targets. Therefore, we used a model of neonatal rat cardiomyocytes and precipitated sheared chromatin samples with 5µg of MEF2 Ab.
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  • Natural Killer Gene Complex (NKC)-encoded immunomodulatory C-type lectin-like receptors (CTLR) include members of the NKRP1 and CLEC2 gene families, which constitute genetically linked receptor-ligand pairs and are thought to allow for NK cell-mediated immunosurveillance of stressed or infected tissues. The mouse CTLR Nkrp1g was previously shown to form several receptor-ligands pairs with the CLEC2 proteins Clr-d, Clr-f, and Clr-g, respectively. Recently, we demonstrated a gut-restricted expression of Clr-f on intestinal epithelial cells that is spatially matched by Nkrp1g on subsets of intraepithelial lymphocytes (Leibelt et al., 2015). We now investigated expression and ligand interaction of Nkrp1g in the splenic compartment, and found an exclusive expression of Nkrp1g on a small subset of NK cells that upregulates Nkrp1g after cytokine exposure. To further characterize NKrp1g+ NK cells, we performed microarray analysis of resting Nkrp1g+ versus Nkrp1g- splenic NK cells that were purified by FACsorting. Total RNA isolation was followed by an Affymetrix microarray analysis.
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