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Accession Number: GSE77140 Platform: GPL15433: Illumina HiSeq 1000 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-01 Summary: Gene expression profiles of rescue with wild type or SUMO double mutant TRIM24 after shRNA mediated knockdown of TRIM24 in MCF7 cell line Overall Design: Gene expression profiles of rescue with wild type TRIM24 and SUMO double mutant, 3 replicate each Contact: Name: srikanth appikonda Organization: MD Anderson Cancer Center Address: 1515 Holcombe Blvd Houston 77030 USA Organization: GEO Address: USA
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Accession Number: GSE94340 Platform: GPL571: [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array Organism: Homo sapiens Published on 2018-01-01 Summary: Wnt signaling pathway is thought to have a role in skin fibrosis in Systemic slcerosis. This Randomized, Placebo-Controlled trial examines the effect of beta catenin inhibition on skin expression. We used microarrays to explore gene expression changes in the C82 trial Overall Design: Patietns with diffuse cutaneous systemic sclerosis had biopsis before treatment and at day 28. Contact: Name: Julio C Mantero Organization: Boston University School of Medicine Deparment: Rheumatology Address: 72 E Concord St Boston MA 02118 USA Organization: Affymetrix, Inc. Address: Santa Clara CA 95051 USA Email: geo@ncbi.nlm.nih.gov, support@affymetrix.com Phone: 888-362-2447 Web-Link: http://www.affymetrix.com/index.affx
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Accession Number: GSE59340 Platform: GPL10558: Illumina HumanHT-12 V4.0 expression beadchip Organism: Homo sapiens Published on 2018-01-01 Summary: To generate drug signatures in human A375 melanoma cell lines. A375 cell line was plated at 4 x 105 cells/mL overnight and treated with ciclopirox or crizotinib at 75% inhibitory concentrations (IC75, determined previously at 72h of treatment) or DMSO (vehicle) for 8h or 24h before harvest. Overall Design: To find out whether drug signatures generated in human melanoma cell lines are predictive of outcome in melanoma patients, we generated ciclopirox and crizotinib signatures in cell lines A375 . The expression of drug signatures were then tested by using GSSA (Gene Signature Survival Analysis) method to find out correlation with clinical outcome of melanoma patients. Contact: Name: Wencai Ma Organization: MD Anderson Cancer Center Address: 7455 Fannin st Houston 77054 USA Organization: Illumina Inc. Address: 9885 Towne Centre Drive San Diego CA 92121 USA Email: expression@illumina.com, techsupport@illumina.com Phone: 1 800 809 4566 Web-Link: www.illumina.com
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Accession Number: GSE92440 Platform: GPL18413: Illumina HiSeq 2500 (Danio rerio) Organism: Danio rerio Published on 2018-01-01 Summary: The transcriptome of zebrafish embryos treated with a Nodal signaling inhibitor at sphere stage, which causes neural tube defects, is compared to those treated at 30% epiboly, which does not. Overall Design: Transcriptomic analysis of differential gene expression of key developmental pathways under differing inhibitory treatments. Contact: Name: Marshall Hampton Organization: University of Minnesota Duluth Address: 1117 University Drive Duluth MN 55812 USA Organization: GEO Address: USA
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Accession Number: GSE96540 Platform: GPL13534: Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) Organism: Homo sapiens Published on 2018-01-01 Summary: We aimed to identify epigenetic alterations associated with the development of traditional serrated adenomas (TSAs). Through DNA methylation analysis with HumanMethylation450 BeadChip in TSAs and sessile serrated adenoma/polyp (SSA/Ps), we identified DNA methylation specifically associated with TSA development. Overall Design: We compared the methylation status between the protruding and flat components of the TSAs, and identified a series of CpG sites which were highly methylated in the protruding portions. We then compared the methylation status of the selected CpG sites between the protruding TSAs and SSA/Ps, and identified a set of CpG sites that were predominantly methylated in protruding TSAs. Contact: Name: Eiichiro Yamamoto Organization: Sapporo medical university Address: South-1, West-16, Chuo-ku Sapporo Japan Email: eiichiro@xa3.so-net.ne.jp Phone: +81-11-611-2111 Organization: Illumina Inc. Address: 9885 Towne Centre Drive San Diego CA 92121 USA Email: expression@illumina.com, techsupport@illumina.com Phone: 1 800 809 4566 Web-Link: www.illumina.com
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Accession Number: GSE104350 Platform: GPL20702: SABiosciences RT2 Profiler Epithelial-Mesenchymal Transition PCR Array Organism: Homo sapiens Published on 2018-01-01 Summary: Comparison of genes associated with the EMT between cytotrophoblast cells (CTB) and extravillous trophoblast cells (EVT) from normal third trimester placenta and abnormally invasive placenta (AIP) Overall Design: EMT-associated genes compared between (a) CTB and EVT from normal thrd trimester placenta (b) EVT from normal third trimester placenta and EVT from placenta previa (c) EVT from placenta previa and AIP (d) CTB from placenta previa and AIP Contact: Name: Nick Illsley Organization: Hackensack University Medical Cednter Laboratory: Center for Abnormal Placentation Deparment: Obstetrics and Gynecology Address: 30 Propspect Ave Hackensack NJ 07601 USA Email: nillsley@hackensackumc.org Phone: +1-551-996-8122 Name: Nicholas P Illsley
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Accession Number: GSE64650 Platform: GPL7202: Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version) Organism: Mus musculus Published on 2018-01-01 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series Contact: Name: Xin Lu Organization: Universität Regensburg Address: Universitätsstr.31 Regensburg 93053 Germany Organization: Agilent Technologies Address: Palo Alto CA 94304 USA Email: cag_sales-na@agilent.com Phone: 877-424-4536 Web-Link: www.agilent.com
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Accession Number: GSE65160 Platform: GPL13112: Illumina HiSeq 2000 (Mus musculus) GPL17021: Illumina HiSeq 2500 (Mus musculus) GPL18635: Ion Torrent Proton (Mus musculus) Organism: Mus musculus Published on 2018-01-01 Summary: We developed a novel single-cell RNA-Seq technique that can directly measure the technical noises for each individual gene by splitting a single cell into two equal halves and measuring their transcriptomes separately (Measure a single cell twice by RNA-Seq, MAST-Seq).The MAST-Seq protocol was developed from the single cell RNA-Seq technique we previously developed (Tang et al. 2010). We first lysated the cell to release the RNA from the cell, then reverse transcripted the mRNA into cDNA, added polyA to the 3' end of cDNA, synthesized the second strand of cDNA used designed primer, and at last PCR amplified the double strand cDNA to get enough amount of DNA to construct the cDNA libraries. Overall Design: 10 single mouse ES cells, 4 half of single mouse ES cells, 4 quarter of single mouse ES cells, 8 eighth of single mouse ES cells, 4 quarter of 2 single mouse ES cells, 4 quarter of 2 single MEF cells,5 single mouse inner cell mass cells, 5 mouse trophectoderm cells, 4 half of single zygotes, 12 half of single 2-cell embryo blastomeres, 24 half of single 4-cell embryo blastomeres, 8 eighth of 8-cell embryo and 64 half of single 8-cell embryo blastomeres, in total 156 samples. Contact: Name: Lu Yang Organization: Peking University Address: YiHeyuan Road No.5 Peking University Beijing Beijing China Email: lucyyang1991@foxmail.com Phone: +86 13810247699 Organization: GEO Address: USA
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Accession Number: GSE99070 Platform: GPL10558: Illumina HumanHT-12 V4.0 expression beadchip Organism: Homo sapiens Published on 2018-01-01 Summary: We characterized tumor and immune microenvironment (TiME) of malignant pleural mesothelioma (MPM) using immunoproteomic approach to comprehensively understand the landscape to affect prognosis and possibly to predict response to immunotherapy. Time-of-Flight Mass Cytometry (CyTOF) was performed on the tumors of 12 MPM patients. We comprehensively analyzed TiME by developing intuitive models for visualizing single-cell data with statistical inference and performed unsupervised clustering of cell frequency. A clinically relevant protein signature through mass spectrometry and mRNA transcriptome array was tested for its ability to reflect prognosis in three independent cohorts (n=330) and to predict response to immune checkpoint inhibitor therapy in publicly available data and in 10 patients of MPM treated with anti-PD1 therapy. A systematic understanding of antitumor immunity by immunoproteomic characterization of TiME envisions significant progress in developing rational immunotherapeutic strategies in MPM. Overall Design: Pre-clinical study Contact: Name: Hyun-Sung Lee Organization: BAYLOR COLLEGE OF MEDICINE Laboratory: ABBR R651H Deparment: Surgical Research Address: One Baylor Plaza HOUSTON TX 77030 USA Email: hyun-sung.lee@bcm.edu Phone: 7137988010 Organization: Illumina Inc. Address: 9885 Towne Centre Drive San Diego CA 92121 USA Email: expression@illumina.com, techsupport@illumina.com Phone: 1 800 809 4566 Web-Link: www.illumina.com
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Accession Number: GSE86280 Platform: GPL17021: Illumina HiSeq 2500 (Mus musculus) Organism: Mus musculus Published on 2018-01-01 Summary: Exposure to ionizing radiation increases the risk of chronic metabolic disorders such as insulin resistance and type 2 diabetes later in life. We hypothesized that irradiation reprograms the epigenome of metabolic progenitor cells, which could account for impaired metabolism after cancer treatment. C57Bl/6 mice were treated with a single dose of irradiation and subjected to high fat diet (HFD). RNA Sequencing and Reduced Representation Bisulfite Sequencing were used to create transcriptomic and epigenomic profiles of preadipocytes and skeletal muscle satellite cells collected from irradiated mice. Mice subjected to total body irradiation showed alterations in glucose metabolism and, when challenged with HFD, marked hyperinsulinemia. Insulin signaling was chronically disrupted in skeletal muscle and adipose progenitor cells collected from irradiated mice and differentiated in culture. Epigenomic profiling of skeletal muscle and adipose progenitor cells from irradiated animals revealed substantial DNA methylation changes, notably for genes regulating the cell cycle, glucose/lipid metabolism and expression of epigenetic modifiers. Our results show that total body irradiation alters intracellular signaling and epigenetic pathways regulating cell proliferation and differentiation of skeletal muscle and adipose progenitor cells, and provide a possible mechanism by which irradiation used in cancer treatment increases the risk for metabolic disease later in life. Overall Design: Reduced representation bisulfite sequencing (RRBS), RNA-Seq and Methyl-CpG-binding domain sequencing (MBD-Seq) of SVF and satellite cells, on CHOW or HFD and untreated or irradiated  Contact: Name: Lars Roed Ingerslev Organization: Copenhagen University Laboratory: Integrative Physiology Deparment: NNF Center for Basic Metabolic Research Address: Blegdamsvej 3B Copenhagen Denmark Email: ingerslev@sund.ku.dk Organization: GEO Address: USA
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