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RNA extraction and microarray analysis total RNA from immortalized normal mammary epithelial cells (184A1, MCF-12A), breast cancer cells (MDA-MB-231, MCF-7, MDA-MB-468, SK-BR-3), BCSC (MDA-MB-231SC, MCF-7SC, XM322, XM607). MDA-MB-231SC and MCF-7SC originating from breast cancer cell lines; XM322 and XM607 derived from clinical specimens which had been described in previous submission (E-MTAB-5057). The miRNA profiling was performed using Agilent miRNA array. Microarray experiments were conducted according to the manufacturer's instructions. To select the differentially expressed genes, we used threshold values of ≥ 2 and ≤ −2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of Cluster 3.0 software then further analyzed with hierarchical clustering with average linkage (genes which value more than 100 were evaluated).
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Alzheimer’s disease (AD) is an aging related neurodegenerative pathology that affects millions of people worldwide. This pathology has been related to a range of features such as deposition of proteins in the brain, alterations in cell cycle, accumulation of DNA damage, DNA repair deficiency and mitochondrial dysfunction, however the molecular mechanisms implicated in its pathogenesis are still uncertain. Thereby, the present study aimed to evaluate whether peripheral blood mononuclear cells (PBMCs) of AD patients display alterations in gene expression profilescompared to age-matched controls. Blood samples were collected from 25 AD patients and 15 age-matched controls in order to perform genome-wide mRNA expression (microarray). In blood cells, Rank products bioinformatics analysis indicated 593 mRNAs adifferentially expressed in AD compared to controls. Our results demonstrated that PBMCs have alterations in cell cycle and DNA repair as proposed for AD neurons, reinforcing the idea that AD blood cells can provide information about AD status and also can be import as source of studies to better understand the disease.
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Somitogenesis is the segmentation of the developing embryonic body axis into somites and is guided by oscillating genes, which create waves of expression that travel across the presomitic mesoderm (PSM) from posterior to anterior. Upon arrival of a wave at the PSM's anterior end, a new somite is formed. To identify genes that are expressed in a wave-like pattern we dissected the PSM of four different mouse embryos (pre-turned), separated the left and right sides, and divided each into five segments, from posterior to anterior (sampling sites 1 to 5). Each segment was used to construct libraries for high-throughput RNA-sequencing. For one embryo, we also sequenced two somites.
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Gastrulation represents a pivotal point in mammalian development, when the basic body plan is established and cells are specified into one of the three germ layers. This is followed by rapid diversification into specific lineages and the appearance of the various cell types required to build each of the organs. The rich variety of cell types present at this stage has never been rigorously characterised in any mammalian organism, and thus insight into cell fate decisions and the underlying regulatory networks have been inaccessible. We have used droplet based single-cell RNA-sequencing to address this by profiling ~7000 cells from three E8.25 mouse embryos.
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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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