GSE109901 Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Drosophila melanogaster ; Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Drosophila melanogaster Mus musculus Source Type: research

GSE112213 Next Generation Sequencing of LdlrKO LXR α-phosphorylation disrupted macrophage transcriptomes
This study aims to as sess changes in bone marrow derived macrophage transcriptional profiles of mice that carry LysMcre directed phosphorylation deficient-version of LXRα compared (S196A) to wild-type (WT). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE112616 Transcriptomic signature of hepatocellular carcinoma and intrahepatic cholangiocarcinoma derived from oncogenically transformed murine hepatocytes after stable knock-down of Tbx3 or Prdm5
Contributors : Lars Zender ; Marco Seehawer ; Florian Heinzmann ; Oliver Bischof ; Pierre-Francois Roux ; Gregory Dore ; Nir RozenblumSeries Type : Expression profiling by arrayOrganism : Mus musculusPrimary liver cancer represents a major health problem. It comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), which differ markedly with regards to their morphology, metastatic potential and therapy response. Yet, molecular actors and tissue context that commit transformed hepatic cells towards HCC or ICC are largely unknown. Here, we report that the hepatic microenvironment epigenetically shap...
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE112617 Transcriptomic and epigenetic signatures of hepatocellular carcinoma and intrahepatic cholangiocarcinoma derived from oncogenically transformed murine hepatocytes
Series Type : Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE113028 LGP2 virus sensor regulates microRNA-mediated gene expression network by interacting with an RNA silencing enhancer, TRBP.
Contributor : Kumiko Ui-TeiSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo reveal the fuction of cytoplasmic virus sensor protein, LGP2, on RNA silencing, we analyzed gene expression profiles on HeLa WT and LGP2 knockout cells, which were generated with CRISPR/Cas system. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE113619 Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation [RNA-seq]
Contributors : Alexandros Onoufriadis ; Chao K Hsu ; Chrysanthi Ainali ; Chuin Y Ung ; Ellie Rashidghamat ; Hsing-San Yang ; Hsin-Yu Huang ; Umar Niazi ; Jui-Chu Yang ; Rosamond Nuamah ; Alka Saxena ; Emanuele de Rinaldis ; John A McGrathSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensKeloids represent a common form of exaggerated wound scarring that cause considerable morbidity. Moreover, there are limited data on molecular mechanisms underlying keloids and effective therapies are lacking. To gain new insight in the transcriptomic alterations of wound healing in keloid-prone individu...
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113620 Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation [miRNA]
Contributors : Alexandros Onoufriadis ; Chao-Kai Hsu ; Chrysanthi Ainali ; Chuin Y Ung ; Ellie Rashidghamat ; Hsing-San Yang ; Hsin-Yu Huang ; Umar Niazi ; Jui-Chu Yang ; Rosamond Nuamah ; Alka Saxena ; Emanuele de Rinaldis ; John A McGrathSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiens ; synthetic constructKeloids represent a common form of exaggerated wound scarring that cause considerable morbidity. Moreover, there are limited data on molecular mechanisms underlying keloids and effective therapies are lacking. To gain new insight in the transcriptomic alterations of wound healing in keloid-prone i...
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens synthetic construct Source Type: research

GSE113621 Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation
Series Type : Non-coding RNA profiling by array ; Expression profiling by high throughput sequencingOrganism : Homo sapiens ; synthetic constructThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Expression profiling by high throughput sequencing Homo sapiens synthetic construct Source Type: research

GSE114711 Tissue and exosomal miRNA editing in Non-Small Cell Lung Cancer
Contributors : M Acunzo ; P S Nana-SinkamSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensWe analyzed small-RNA sequencing data from plasma-derived exosome (PEV) from a cohort of NSCLC patients at different stages.We identified two ED miRNAs in circulation able to distinguish between normal and tumor sample subtypes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116134 Tesmall indentifies small RNAs associated with targeted inhibitor resistance in melanoma
Contributors : Kathryn O'Neill ; Molly G HammellSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensMicroRNAs (miRNAs) are small 21-22nt RNAs that act to regulate the expression of mRNA target genes through direct binding to mRNA targets. While miRNAs typically dominate small RNA transcriptomes, many other classes are present including tRNAs, snoRNAs, snRNAs, Y-RNAs, piRNAs, and siRNAs. Interactions between processing machinery and targeting networks of these various small RNA classes remains unclear, largely because these small RNAs are typically analyzed separately. Here we present ...
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116378 Genetic vulnerability to DUSP22 promotor hypermethylation is involved in the relation between in utero famine exposure and schizophrenia (DUTCHSCZ Data Set)
Contributor : Marco P BoksSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensEpigenetic changes may account for the doubled risk to develop schizophrenia in individuals exposed to famine in utero. We therefore investigated DNA methylation in a unique sample of patients and healthy individuals conceived during the great famine in China. Subsequently we examined two case-control samples without famine exposure in whole blood and brain tissue. To shed light on the causality of the relation between famine exposure and DNA methylation we exposed human fibroblasts to nutritional deprivation. In the ...
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE116379 Genetic vulnerability to DUSP22 promotor hypermethylation is involved in the relation between in utero famine exposure and schizophrenia (CHINFAM Data Set)
Contributor : Marco P BoksSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensEpigenetic changes may account for the doubled risk to develop schizophrenia in individuals exposed to famine in utero. We therefore investigated DNA methylation in a unique sample of patients and healthy individuals conceived during the great famine in China. Subsequently we examined two case-control samples without famine exposure in whole blood and brain tissue. To shed light on the causality of the relation between famine exposure and DNA methylation we exposed human fibroblasts to nutritional deprivation. In the ...
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE116380 Genetic vulnerability to DUSP22 promotor hypermethylation is involved in the relation between in utero famine exposure and schizophrenia
Series Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE116383 Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ATAC-seq]
Contributors : Geoffrey Wahl ; Chi-Yeh Chung ; Christopher DravisSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe performed ATAC-seq on normal mammary cell populations and mouse mammary tumor cell populations (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE116384 Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ChIP-seq]
Contributors : Geoffrey Wahl ; Chi-Yeh Chung ; Christopher DravisSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe performed H3K27ac ChIP-seq on normal mammary cell populations and SOX10 ChIP-seq on PY230 tumors (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE116385 Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [RNA-seq]
Contributors : Geoffrey Wahl ; Chi-Yeh Chung ; Christopher DravisSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed RNA-seq on normal mammary cell populations and mouse mammary tumor cell populations (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116386 Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116398 Effect of arsenate and arsenite on Lysinibacillus sp. B2A1 transcriptome
Contributors : Jagat Rathod ; Jiin-Shuh JeanSeries Type : Expression profiling by high throughput sequencingOrganism : Lysinibacillus sp. B2A1RNA-seq based indentification of arsenic responsive genes which might provide resistance and are involved (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Lysinibacillus sp. B2A1 Source Type: research

GSE116414 AffymetrixHuman Gene 2.0 ST Array
Contributors : V Gouaze-Andersson ; C ToulasSeries Type : Expression profiling by arrayOrganism : Homo sapiensGene expression in glioblastoma cells from patients before treatment. The cells were inhibited or not for FGFR1.Glioblastoma are known to be aggressive and therapy-resistant tumors, due to the presence of glioblastoma stem cells (GSC) inside this heterogeneous tumor. We investigate here the involvement of FGFR1 in glioblastoma stem-like cells (GSLC) radioresistance mechanisms. We first demonstrated that the survival after irradiation was significantly diminished in FGFR1-silenced (FGFR1-) GSLC compared to control G...
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE116422 The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size
Contributor : Lu B TanSeries Type : Expression profiling by high throughput sequencingOrganism : Oryza sativa Indica GroupThe APETALA2-like transcription factor SUPERNUMERARY BRACT confers seed shattering by positively regulating qSH1 and SH5, while altering seed size by modulating longitudinal cell elongation in rice glumes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Indica Group Source Type: research

GSE116366 RNAseq of Maize stem at big flare period
Contributors : Hengsheng Wang ; Beijiu ChengSeries Type : Expression profiling by high throughput sequencingOrganism : Zea maysFour samples from the low and high hybrid at big flare period were used for RNA sequencing. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Zea mays Source Type: research

Gse90525 generation of hepatic stellate cells by directed differentiation of human pluripotent stem cells
Contributors : M Coll ; L Perea ; J J Lozano ; P SanchoSeries Type : Expression profiling by arrayOrganism : Homo sapiensHepatic stellate cells (HSC) are the main stromal cell component of the liver. In healthy liver, quiescent HSC participate in the homeostasis of extracellular matrix (ECM) and store vitamin A. Liver injury causes HSC activation, where they participate in the wound-healing response, by producing ECM components as well as cytokines involved in liver regeneration and inflammation. Moreover, HSC are the main cell type responsible for fibrosis progression. The lack of homogeneous cultures and renewable source...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE93050 Tumor suppressor functions of DAXX through histone H3.3 deposition pathway in pancreatic neuroendocrine tumor
Conclusions: DAXX plays as a tumor suppressor and DAXX/H3.3 complex suppresses target genes by promoting H3K9me3 in PanNETs. DAXX and its target molecule might be effective biomarkers and therapeutic candidates. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE100640 DREAM of MDA-MB-231 cells with TET1 knockout
Contributors : Charly R Good ; Shoghag Panjarian ; Andrew D Kelly ; Jozef Madzo ; Bela Patel ; Jaroslav Jelinek ; Jean-Pierre IssaSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensDNA hypermethylation is known to contribute to the formation of cancer. However, DNA hypomethylation has received far less attention and the factors controlling the balance between hypo and hypermethylation and its impact on tumorigenesis remains unclear. Triple negative breast cancer (TNBC), a subtype of breast cancer that does not overexpress the hormone receptors or HER2/NEU, is one of the most hypomethyla...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104320 PP1-NIPP1 wild type and mutant overexpression in Flip-In ™ T-Rex Hela cells
Contributors : Claudia Winkler ; Aleyde Van EyndeSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNAi-seq of stable Flp-In ™ T-Rex Hela cells that inducibly expressed PP1-NIPP1 and mutants. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111602 Defects in the alternative splicing-dependent regulation of REST cause deafness - [mouse brain cortex].
Contributors : Yoko Nakano ; Michael C Kelly ; Atteeq U Rehman ; Erich T Boger ; Robert J Morell ; Matthew W Kelley ; Thomas B Friedman ; Botond B ánfiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe DNA-binding protein REST forms complexes with histone deacetylases (HDACs) to repress neuronal genes in non-neuronal cells. In differentiating neurons, REST is downregulated predominantly by transcriptional silencing. Here we report that post-transcriptional inactivation of REST by alternative splicing is required for hearing in humans and mice. We show that in the mechanosensor...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111603 Defects in the alternative splicing-dependent regulation of REST cause deafness - [mouse cultured organ of Corti].
Contributors : Yoko Nakano ; Michael C Kelly ; Atteeq U Rehman ; Erich T Boger ; Robert J Morell ; Matthew W Kelley ; Thomas B Friedman ; Botond B ánfiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe DNA-binding protein REST forms complexes with histone deacetylases (HDACs) to repress neuronal genes in non-neuronal cells. In differentiating neurons, REST is downregulated predominantly by transcriptional silencing. Here we report that post-transcriptional inactivation of REST by alternative splicing is required for hearing in humans and mice. We show that in the mechanosensor...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111604 Defects in the alternative splicing-dependent regulation of REST cause deafness - [mouse utricles].
Contributors : Yoko Nakano ; Michael C Kelly ; Atteeq U Rehman ; Erich T Boger ; Robert J Morell ; Matthew W Kelley ; Thomas B Friedman ; Botond B ánfiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe DNA-binding protein REST forms complexes with histone deacetylases (HDACs) to repress neuronal genes in non-neuronal cells. In differentiating neurons, REST is downregulated predominantly by transcriptional silencing. Here we report that post-transcriptional inactivation of REST by alternative splicing is required for hearing in humans and mice. We show that in the mechanosensor...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111606 Defects in the alternative splicing-dependent regulation of REST cause deafness
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE112212 Nucleotide resolution genome-wide mapping of 8-oxoG damage
Contributors : Junzhou Wu ; Shana J SturlaSeries Type : OtherOrganism : Saccharomyces cerevisiae BY4741Single nucleotide resolution sequencing of DNA damage is required to decipher the complex causal link between the identity and location of DNA adduct and mutation patterns in the genome. We coupled the specificity of the repair enzyme with the efficiency of a one-pot click-DNA ligation reaction to insert a readable oligonucleotide code sequence. The biocompatible code enabled high-throughput, base resolution sequencing of the 8-oxoguanine site and thus have named the method click-code-seq. By applying click-code-seq to a ...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Other Saccharomyces cerevisiae BY4741 Source Type: research

GSE114724 Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing
Contributors : Elham Azizi ; Ambrose J Carr ; George Plitas ; Andrew E Cornish ; Catherine Konopacki ; Sandhya Prabhakaran ; Juozas Nainys ; Kenmin Wu ; Vaidotas Kiseliovas ; Manu Setty ; Kristy Choi ; Rachel M Fromme ; Phuong Dao ; Peter T McKenney ; Ruby C Wasti ; Krishna KadaveruSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensKnowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114725 Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 3' RNA Sequencing
Contributors : Elham Azizi ; Ambrose J Carr ; George Plitas ; Andrew E Cornish ; Catherine Konopacki ; Sandhya Prabhakaran ; Juozas Nainys ; Kenmin Wu ; Vaidotas Kiseliovas ; Manu Setty ; Kristy Choi ; Rachel M Fromme ; Phuong Dao ; Peter T McKenney ; Ruby C Wasti ; Krishna Kadaveru ; Linas Mazutis ; Alexander Y Rudensky ; Dana Pe ’erSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensKnowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer u...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114727 Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115685 DNA methylation analysis of breast cancer Hs578T cells with TET1 knockout
Contributors : Charly R Good ; Shoghag Panjarian ; Andrew D Kelly ; Jozef Madzo ; Bela Patel ; Jaroslav Jelinek ; Jean-Pierre IssaSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensBoth gains and losses of DNA methylation are common in cancer but the factors controlling this methylation balance remain unclear. Triple negative breast cancer (TNBC), a subtype that does not overexpress hormone receptors or HER2/NEU is one of the most hypomethylated cancers observed. In search for an explanation for this, we discovered that the TET1 DNA demethylase is specifically overexpressed in about 40%...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115696 DNA methylatioin analysis of breast cancer cell lines with TET1 knockout
Series Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116322 Expression data from rice inflorescences of osmads32 mutant and wild type
Contributor : Yun HuSeries Type : Expression profiling by arrayOrganism : Oryza sativaMADS family genes in rice control flowering and inflorescence development. In the early flower stages of plant, MADS-box transcripion factors could form protein-protein interaction complexes with other floral homeotic genes and regulate the expression of downstram genes. OsMADS32 in rice is an important transcription factor in controlling flower developmentWe used microarrays to detail the expression of downstream genes under the control of OsMADS32 during the early inflorescence stages in rice (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Oryza sativa Source Type: research

GSE116324 RNA-Seq of newly diagnosed patients in the PADIMAC study leads to a bortezomib/lenalidomide decision signature
Contributor : Mike ChapmanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensImproving outcomes in multiple myeloma will not only involve development of new therapies, but better use of existing treatments. We performed RNA sequencing (RNA-Seq) on samples from newly diagnosed patients enrolled into the phase II PADIMAC study. Using an empirical Bayes approach and synthetic annealing, we developed and trained a seven-gene signature to predict treatment outcome. We tested the signature on independent cohorts treated with bortezomib- and lenalidomide-based therapies. The signature was capab...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116326 Transcriptome changes of whole kidney from conditional Vhl gene knockout in sub-populations of mouse kidney tubule cells
Contributors : Hannah L Bader ; Tien HsuSeries Type : Expression profiling by arrayOrganism : Mus musculusWe are studying a tumor suppressor gene, von Hippel-Lindau (VHL). In humans, VHL mutations cause renal cell carcinoma of the clear cell type (ccRCC). We have generated a knockout mouse strain in which mouse Vhl is conditionally deleted in the kidney epithelium (that is, a subset of tubules including collecting ducts and ascending loop of Henle). Instead of ccRCC, these mice developed severe inflammation and fibrosis, accompanied by hyperplasia and the appearance of transformed clear cells. These phenotypes therefore su...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116347 Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types.
We reported transcriptional characterization of tumor-infiltrating T regulatory cells (TITRs) that is shared between species and among different tumor types and stages. We genomically profiled immunocytes from 2 species: 1. Mouse: CD4+ Treg and Tconv, and CD8+ T cells from tumor and spleen of B16, MC38 or CT26 tumor bearing mice, as well as from spleens of non-tumor bearing mice. 2. Human: CD4+ Treg cells from surgically resected and cryopreserved human colorectal carcinomas or normal colon tissue. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE116348 The effect of cellular context on miR-155 mediated gene regulation in four major immune cell types (RNA-Seq)
Contributor : Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNumerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3 ’UTR usage analysis using poly...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116350 Endothelial Cell CD36 Optimizes Tissue Fatty Acid Uptake
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMovement of circulating fatty acids (FAs) to parenchymal cells requires their transfer across the endothelial cell (EC) barrier. The multi-ligand receptor cluster of differentiation 36 (CD36) facilitates tissue FA uptake and is expressed in ECs and parenchymal cells such as myocytes and adipocytes. Whether tissue uptake of FAs is dependent on EC or parenchymal cell CD36, or both, is unknown. Using a cell-specific deletion approach, we show that CD36-mediated FA transport across ECs rate-limits tissue FA uptake, and its loss leads to meta...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116361 Hierarchal gene master regulators of adenocarcinomic human alveolar basal epithelial cells A549.
Contributors : Dumitru A Iacobas ; Sanda Iacobas ; Katrien Van Roosbroeck ; George A CalinSeries Type : Expression profiling by arrayOrganism : Homo sapiensIn previous papers we proved that cancer nodules and surrounding normal tissue are governed by different gene master regulators (GMRs) and that expression manipulation of a cancer GMR can selectively destroy cancer cells with minimal effects on the normal ones. GMR is defined as a coding or non-coding transcript whose strictly controled abundance by the cell homeostatic mechanisms regulates most major cell functional pathways. Here, we determined the gene hierarchy in t...
Source: GEO: Gene Expression Omnibus - June 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE116246 Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources
Contributors : Abbas Jariani ; Bram CerulusSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeTranscriptome of S. cerevisiae in shifts between glucose and maltose media with different re-growth conditions (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE58469 Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines (microRNAs)
Contributors : Loris De Cecco ; Laura Gatti ; Noemi Arrighetti ; Giacomo Cossa ; Paola PeregoSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensResistance to platinum compounds represents a major obstacle to the cure of ovarian carcinoma. The molecular profiling of drug-sensitive and drug-resistant cells may be helpful to clarify if altered expression of miRNAs can contribute to the drug-resistant phenotype. The expression pattern of miRNAs of three ovarian carcinoma cell lines was examined. The analysis revealed the modulation of several miRNAs in the two platinum-resistant cell lines as compared to par...
Source: GEO: Gene Expression Omnibus - June 26, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE58470 Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines (gene expression)
Contributors : Loris De Cecco ; Laura Gatti ; Noemi Arrighetti ; Giacomo Cossa ; Paola PeregoSeries Type : Expression profiling by arrayOrganism : Homo sapiensResistance to platinum compounds represents a major obstacle to the cure of ovarian carcinoma. The molecular profiling of drug-sensitive and drug-resistant cells may be helpful to clarify if altered gene expression can contribute to the drug-resistant phenotype. The expression pattern of three ovarian carcinoma cell lines was examined. The analysis revealed the modulation of several genes in the two platinum-resistant cell lines as compared to parental platinum-sensi...
Source: GEO: Gene Expression Omnibus - June 26, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE58472 Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines
Series Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 26, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE65459 Knockdown of TSPAN8 gene expression in the SH-SY5Y neuroblastoma cell line
Contributors : Christoph Schartner ; Heike Weber ; Claus J Scholz ; Florian Freudenberg ; Antonia Post ; Lena Wei ßflog ; Andreas ReifSeries Type : Expression profiling by arrayOrganism : Homo sapiensBipolar disorder (BD) has an estimated heritability of about 80%. Different pathways and candidate genes may contribute to the pathogenesis of BD, but definite mechanisms are yet unresolved. In a previous study, we identified the single nucleotide polymorphism (SNP) rs4500567, located in the upstream region of Tetraspanin 8 (TSPAN8), to be associated with bipolar disorder (BD).The SNP ´s minor allele results in a p...
Source: GEO: Gene Expression Omnibus - June 26, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE75972 DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [Bisulfite-seq]
Contributors : Heather J Lee ; Steffen Rulands ; Stephen J Clark ; Christof Angermueller ; Sebastien A Smallwood ; Felix Krueger ; Gavin Kelsey ; Oliver Stegle ; Benjamin D Simons ; Wolf ReikSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusMouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that ...
Source: GEO: Gene Expression Omnibus - June 26, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE75973 DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [PBAT Bisfulfite-seq]
Contributors : Steffen Rulands ; Heather J Lee ; Stephen J Clark ; Christof Angermueller ; Sebastien A Smallwood ; Felix Krueger ; Gavin Kelsey ; Oliver Stegle ; Benjamin D Simons ; Wolf ReikSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusMouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that ...
Source: GEO: Gene Expression Omnibus - June 26, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE75974 DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [single cell Bisulfite-seq]
Contributors : Steffen Rulands ; Heather J Lee ; Stephen J Clark ; Christof Angermueller ; Sebastien A Smallwood ; Felix Krueger ; Gavin Kelsey ; Oliver Stegle ; Benjamin D Simons ; Wolf ReikSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusMouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that ...
Source: GEO: Gene Expression Omnibus - June 26, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research