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GSE98206 MALT1 Inhibition Is Efficacious in Both Na ïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia.
Contributors : Nakhle S Saba ; Deanna Wong ; Georges Tanios ; Jessica Iyer ; Patricia Lobelle-Rich ; Eman Dadashian ; Delong Liu ; Lorena Fontan ; Erik K Flemington ; Cydney Nichols ; Chingiz Underbayev ; Hana Safah ; Ari Melnick ; Adrian Wiestner ; Sarah E HermanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe clinical efficacy displayed by ibrutinib in chronic lymphocytic leukemia (CLL) has been challenged by the frequent emergence of resistant clones. The ibrutinib target, Bruton's tyrosine kinase (BTK), is essential for B-cell receptor signaling, and most resistant cases carry ...
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100180 Impaired chloroplast biogenesis causes color variation between two varieties/cultivars of Chinese orchid (Cymbidium longibracteatum)
Contributors : Yu Jiang ; Jun-rong He ; Jia LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Cymbidium tortisepalum var. longibracteatumTo explore the mechanisms governing the leaf color variations in Chinese orchids, we analyzed gene expression differences between a wild-type and an albino-type cultivar of Cymbidium longibracteatum (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Cymbidium tortisepalum var. longibracteatum Source Type: research

GSE102810 Intrinsic specificity differences between transcription factor paralogs reveal new insights into interpretation of non-coding mutations [Universal PBM 4x44k]
Contributor : Raluca GordanSeries Type : OtherOrganism : Homo sapiensMembers of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic ...
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE103585 TP53INP2 knockout in perigonadal white adipose tissue
Contributors : Antonio Zorzano ; Montserrat Romero ; Alba Sabat é-PérezSeries Type : Expression profiling by arrayOrganism : Mus musculusExcessive fat accumulation is a major risk factor for the development of type 2 diabetes.To determine the mechanisms by wich TP53INP2 regulates adipogenesis, gene expression profile was performed in perigonadal white adipose tissue fromTP53INP2-deficient mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE103586 TP53INP2 knockout in inguinal white adipose tissue
Contributors : Antonio Zorzano ; Montserrat Romero ; Alba Sabat é-PérezSeries Type : Expression profiling by arrayOrganism : Mus musculusExcessive fat accumulation is a major risk factor for the development of type 2 diabetes.To determine the mechanisms by wich TP53INP2 regulates adipogenesis, gene expression profile was performed in inguinal white adipose tissue fromTP53INP2-deficient mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE103587 TP53INP2 knockout in perigonadal and inguinal white adipose tissue
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 - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104599 A regulon enrichment test reveals the activation of major regulators of Mycobacterium tuberculosis gene expression in two models of antibiotic tolerance.
Contributors : Petros C Karakousis ; Dalin Rifat ; William MaternSeries Type : Expression profiling by high throughput sequencingOrganism : Mycobacterium tuberculosisThe acquisition of microbial antibiotic tolerance is suspected to be a major factor in the lengthy duration of current Tuberculosis therapies. We model antibiotic tolerance in vitro by exposing Mycobacterium tuberculosis to two distinct stress conditions: hypoxia and nutrient starvation (PBS). We then measured the bacterial transcriptional response with RNA-seq. We employed a bioinformatics approach to identify important transcriptional regulators of the respo...
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mycobacterium tuberculosis Source Type: research

GSE109833 Global gene expression profile of primary cultured keratinocytes with or without stimulation
Contributors : Miao Xu ; Huiping Lu ; Xiaohong ZhaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSkin tissues from newborn C57BL/6 mice were obtained for primary keratinocyte culture. Cells were then stimulated with or without IL-25 (Biolegend) for 8hrs. Total RNAs were isolated with RNAprep pure Tissue Kit (DP431) and the RNA-seq library was prepared by the Beijing Genomics Institute. Sequence reads were obtained using BGIseq500 (Illumina) and successfully mapped to mouse genome. Reads counts were normalized based on RPKM, fold changes were calculated for all possible comparisons. ...
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110127 Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea
In this study, the root tissues from the salt tolerant genotype (JG 11) and the salt sensitive genotype (ICCV 2) were analyzed using RNA sequencing to identify genes/pathways associated with salt tolerance/sensitivity in the both genotypes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Cicer arietinum Source Type: research

GSE110186 NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn ’s disease patients
Contributors : Holger Sch äffler ; Maria Rohde ; Sarah Rohde ; Astrid Huth ; Nicole Gittel ; Hannes Hollborn ; Dirk Koczan ; Änne Glass ; Georg Lamprecht ; Robert JasterSeries Type : Expression profiling by arrayOrganism : Homo sapiensEmploying microarray assays, a total of 267 genes were identified that were significantly up- or downregulated in PBMCs of WT-NOD2 patients, compared to healthy donors after challenge with vitamin D (+/-D) and/or a combination (+/-LP) of LPS (lipopolysaccharide) and PGN (peptidoglycan) (p
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE110249 Global gene expression profile of CD8+ TILs from WT and B7S1 KO mice
Contributors : Jing Li ; Huiping Lu ; Xiaohong ZhaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusB7S1 negatively regulates T cells and its expression correlates with poor prognosis of cancer patients. In order to understand how B7S1 signaling contributes to dysfunction of CD8+ T cell in the TME, we conducted transcriptional analysis of OVA-specific CD8+ TILs and different TIL subsets from E.G7-bearing WT and B7S1 KO mice (Day 21). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110251 Epigenetic profiling of OVA-specific CD8+ TILs from mice treated with control, anti-B7S1, anti-PD-1 or anti-B7S1+anti-PD-1 antibodies
Contributors : Jing Li ; Yanjian LiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusCombinational blockade of B7S1 and PD-1 exhibits stronger anti-tumor efficacy than monotherapies. In order to further understand the mechanisms whereby blockade of B7S1 or PD-1 inhibits tumor growth, we conducted ATAC-seq analysis of OVA-specific CD8+ TILs from E.G7-bearing mice treated with control antibodies, anti-B7S1, anti-PD-1 monotherapy or combinational therapy. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE110787 Novel Protective Role of Nicotinamide Phosphoribosyltransferase in Acetaminophen-induced Acute Liver Injury in Mice
The objective of this study was to explore the role and mechanisms of nicotinamide phosphoribosyltransferase (NAMPT) in acetaminophen-induced ALI. C57BL/6 Nampt gene wild type (Nampt+/+)-, heterozygous knockout (Nampt+/-)-, and overexpression (NamptOE)-mice were treated with overdose of acetaminophen, followed by histological, biochemical, and transcriptomic evaluation of liver injury. The mechanism of Nampt in acetaminophen -induced hepatocytic toxicity was also explored in cultured primary hepatocytes. Three lines of evidence have convergently demonstrated that acetaminophen overdose triggers the most severe oxidative st...
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110952 Functional studies of missense TREM2 mutations in human stem cell-derived microglia
We describe a robust method for the derivation and maintenance of microglia from human stem cells, which are phenotypically and functionally comparable to primary human microglia. We used stem cell-derived microglia to study the consequences of missense mutations in the microglial-expressed protein Triggering Receptor Expressed on Myeloid cells 2 (TREM2), which are causal for a frontotemporal dementia-like (FTD-like) syndrome and Nasu-Hakola disease (NHD). While many ligands and functions for TREM2 have been described, it is not known how TREM2 signalling dysregulation affects specific elements of microglial biology to inf...
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111968 Transcriptomic analysis of human tonsillar TFH subsets
Contributors : Vinay S Mahajan ; Hamid Mattoo ; Shiv PillaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe used an IL4-capture assay followed by FACS sorting, to isolate IL4-secreting TFH cells from a human tonsil and compared their transcriptomic profiles with CXCR5hi PD1hi IL4-negative tonsillar TFH cells and IL4-producing CXCR5neg non-TFH cells (TH2 cells). Our studies validate the notion of functionally distinct TFH subsets and identify genes that are specifically expressed in and define the human IL-4 secreting TFH cell subset. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112583 Transcriptome of sunflower (Helianthus annuus) nectaries and leaf
Contributors : Clay J Carter ; Jarrad R Prasifka ; Marshall HamptonSeries Type : Expression profiling by high throughput sequencingOrganism : Helianthus annuusComparative RNA-Seq study of expression in sunflower nectaries from different lines. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Helianthus annuus Source Type: research

GSE112596 Epigenome analysis of CD4 T cells from treated and untreated patients with multiple sclerosis (MS)
Contributors : Achilles Ntranos ; Vasilis Ntranos ; Ye He ; Valentina Bonnefil ; Jia Liu ; Yunjiao Zhu ; Rachel Brandstadter ; Corey T Watson ; Andrew J Sharp ; Ilana K Sand ; Patrizia CasacciaSeries Type : Methylation profiling by arrayOrganism : Homo sapiensGenome wide DNA methylation profiling of CD4 T cells from treated and untreated patients with multiple sclerosis. The Illumina InfiniumEPIC methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs of CD4 T cells from patients with multiple sclerosis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE112610 C. elegans: total mRNA vs. AWA-specifc mRNA
Contributors : King L Chow ; Yuan ZhouSeries Type : OtherOrganism : Caenorhabditis elegansTranscriptional profiling of AWA neurons comparing total mRNA of C. elegansThe aforementioned results provided us a clear indication that a GPCR expressed in AWA would likely be used for pheromone perception. To get a male AWA-specific expression profile, we adopted a poly-A-binding protein (PABP) mRNA pull-down approach to isolate cell-specific genes (Kunitomo et al., 2005) and co-transformed into the worms a sex determination gene, fem-3, to masculinize its nervous system. Ectopic expression of fem-3 in all neurons can change the en...
Source: GEO: Gene Expression Omnibus - April 3, 2018 Category: Genetics & Stem Cells Tags: Other Caenorhabditis elegans Source Type: research

GSE112585 Expression data from healthy murine bronchial epithelial cells and syngeneic murine lung squamous carcinoma (LUSC) from DBA2 mice.
Contributors : Alessandro Porrello ; Chad V PecotSeries Type : Expression profiling by arrayOrganism : Mus musculusThe process of lung squamous carcinoma tumorigenesis and metastasis is poorly characterized. Additionally, few models of this process exist in an immune-competent context. In order to address this problem, we utilized the KLN-205 lung squamous carcinoma cell lines that is derived from carcinogen exposure in DBA2 mice.We used healthy bronchial epithelial cells from adult DBA2 mice as a healthy control. Following an in vivo selection strategy to enrich for metastatic subclones (LN2-2, LN4-2, LN4K1), we used Affy...
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE17835 Comparison of the responses of Mycobacterium tuberculosis and Mycobacterium bovis to nutrient starvation
Contributor : Morad HassaniSeries Type : Expression profiling by arrayOrganism : Mycobacterium bovis ; Mycobacterium tuberculosisTranscriptional profiling of Mycobacterium tuberculosis H37Rv and Mycobacterium bovis Ravenel before (i.e., log-phase control) and at 24h and 96h after nutrient starvation. The transcriptional profile of the two strains were compared at log phase, and after 24h and 96h of starvation. In addition, the response of each strain to starvation was examined after 24h and 96h of starvation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mycobacterium bovis Mycobacterium tuberculosis Source Type: research

GSE95805 Overexpression of PIK3CA in head and neck squamous cell carcinoma is associated with poor outcome and activation of the YAP pathway
Conclusions: High expression of PIK3CA in HNSCC primary tumors identifies patients at high risk for recurrence. In these tumors, progression could rely on the Hippo-YAP pathway instead of the canonical Akt/mTOR pathway. This observation could have important implications in the therapeutic options for patients. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE97504 Expression data of colonic epithelial cells colonized with B. theta
Contributors : Akira Nakajima ; Keiichiro SuzukiSeries Type : Expression profiling by arrayOrganism : Mus musculusThe gut microbiota is essential for several aspects of host physiology such as metabolism, epithelial barrier function and immunity. Previous studies have revealed that host immune system as well as diet and other environmental factors have a strong impact on the composition and activity of gut microbiota, but the molecular requirements for such functional regulation remain unknown. We show that the bacteria belonging to phylum Bacteroidetes acquire their symbiotic activity in the colonic mucus, depending on a ...
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE100274 Chemically Induced Paneth Cells Provide Superior In Vivo Mimic to Organoid-derived Analog
Contributors : Jose Ordovas-Montanes ; Alex K ShalekSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPaneth cells (PCs) are post-mitotic secretory cells of the small intestine that produce antimicrobials, growth factors, and cytokines. Multiple diseases have been linked to alterations in PC function. Past studies of PCs have relied on in vivo models, and limited in vitro models, including organoids. While useful, whether the in vitro models recapitulate in vivo biology is an important, yet unanswered question. Here, we present a bona fide in vitro PC-enriched population derived via che...
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110513 Integrating single-cell transcriptomic data across different conditions, technologies, and species
Contributor : Andrew ButlerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensComputational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple datasets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq datasets based on common sources of variation, enabling the identification of shared populations across datasets and downstream comparative ...
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111863 4C-seq of insulin promoter
We report the 4C (Circularized Chromosome Conformation Capture)-seq data of insulin promoter in EndoC βH1 and HeLa cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE112344 Genome-wide maps of chromatin state in EndoC- βH1 Cells 
We report the actively transcribed chromatin regions in EndoC- βH1 Cells that are associated with histone H3 lysine 27 acetylation mark. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112345 Viral shRNA Knockdown of INS Promotor Activity in EndoC- βH1 Cells 
Contributors : Xing Jian ; Gary FelsenfeldSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo inhibit INS expression, we used shRNA to target the INS promoter. We find that knocking down INS expression with such an shRNA targeting the INS promoter significantly affects expression of 259 genes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112579 Transcriptome of tumor biopsy sample of patient with multiple metachronous ovarian cancer
Contributors : Maria Suntsova ; Elena Ilnitskaya ; Maksim Sorokin ; Anton BuzdinSeries Type : Expression profiling by array ; Third-party reanalysisOrganism : Homo sapiensWe profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) tumor biopsy sample of patient with multiple metachronous ovarian cancer. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Third-party reanalysis Homo sapiens Source Type: research

GSE112580 Transcriptomic comparison of Botrytis cinerea wild type and VELVET mutants
Contributors : Nathalie M üller ; Matthias HahnSeries Type : Expression profiling by high throughput sequencingOrganism : Botrytis cinereaAn RNAseq-based transcriptomic comparison of Botrytis cinerea wild type and the three VELVET mutants was performed, to correlate common virulence defects of the mutants with changes in gene expression. A large number of genes encoding infection-related and secreted proteins was strongly underexpressed in the mutants, in particular genes encoding proteases and carbohydrate active enzymes. Many VELVET-regulated genes were found to be upregulated in the wild type during host plant infe...
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Botrytis cinerea Source Type: research

GSE112582 Gene expression signature of brown and inguinal white fat of mice kept at 30 °C vs. 5°C
Contributors : Martin Jastroch ; Fabiana Perocchi ; Yiming Cheng ; Susanne KeipertSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusActivation and recruitment of thermogenic cells in human white adipose tissues ( “browning”) can counteract obesity and associated metabolic disorders. However, quantifying the effects of therapeutic interventions on browning remains enigmatic. Here, we devise a computational approach, profiling of fat tissue types (ProFAT), for the quantification of thermogenic potential of heterogeneous fat biopsies based on the prediction of white and brown a...
Source: GEO: Gene Expression Omnibus - April 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE112562 Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana).
We present several alternative hypotheses that may explain Gloger’s rule pattern of skin pigmentation variation in the Virginia opossum. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Didelphis virginiana Source Type: research

GSE59158 BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (ChIP-Seq 3T3-L1)
Contributors : Sabina Benko ; Fan Zhang ; Blanca Andino ; Guangtao Zhang ; SiDe Li ; Virginia Gillespie ; Andrew C Shin ; Francesca Aguilo ; Chih-Hung Chen ; Weijia Zhang ; Christoph Buettner ; Ming-Ming Zhou ; Martin J WalshSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusGlucose and fat metabolism are tightly interconnected where endogenous de novo lipogenesis (DNL) serves to convert carbohydrates directly into lipids. Here, we explored the role of the long isoform Brd4 as a key transcriptional co-activator in lipogenesis. As a member of the Bromo-extraterminal (BET) pr...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE59159 BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-Seq 3T3-L1)
Contributors : Sabina Benko ; Fan Zhang ; Blanca Andino ; Guangtao Zhang ; SiDe Li ; Virginia Gillespie ; Andrew C Shin ; Francesca Aguilo ; Chih-Hung Chen ; Weijia Zhang ; Christoph Buettner ; Ming-Ming Zhou ; Martin J WalshSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGlucose and fat metabolism are tightly interconnected where endogenous de novo lipogenesis (DNL) serves to convert carbohydrates directly into lipids. Here, we explored the role of the long isoform Brd4 as a key transcriptional co-activator in lipogenesis. As a member of the Bromo-extraterminal (BET) protein family, ...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE59160 BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-seq Liver)
Contributors : Sabina Benko ; Fan Zhang ; Blanca Andino ; Guangtao Zhang ; SiDe Li ; Virginia Gillespie ; Andrew C Shin ; Francesca Aguilo ; Chih-Hung Chen ; Weijia Zhang ; Christoph Buettner ; Ming-Ming Zhou ; Martin J WalshSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGlucose and fat metabolism are tightly interconnected where endogenous de novo lipogenesis (DNL) serves to convert carbohydrates directly into lipids. Here, we explored the role of the long isoform Brd4 as a key transcriptional co-activator in lipogenesis. As a member of the Bromo-extraterminal (BET) protein family, ...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE59161 BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-seq Fat)
Contributors : Sabina Benko ; Fan Zhang ; Blanca Andino ; Guangtao Zhang ; SiDe Li ; Virginia Gillespie ; Andrew C Shin ; Francesca Aguilo ; Chih-Hung Chen ; Weijia Zhang ; Christoph Buettner ; Ming-Ming Zhou ; Martin J WalshSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGlucose and fat metabolism are tightly interconnected where endogenous de novo lipogenesis (DNL) serves to convert carbohydrates directly into lipids. Here, we explored the role of the long isoform Brd4 as a key transcriptional co-activator in lipogenesis. As a member of the Bromo-extraterminal (BET) protein family, ...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE59162 BRD4 directs glycolytic metabolism through a comprehensive epigenomic and transcriptional network
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy 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 - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE66904 Human OCI-AML3 cells: Control vs. Atg5-shRNA or NPM1-shRNA inducibly expressed
Contributors : Xuhuai Ji ; Min huangSeries Type : Expression profiling by arrayOrganism : Homo sapiensTranscriptional profiling of human OCI-AML3 cells stably expressing inducibly Atg5 shRNA or NPM1-shRNAGoal was to determine the effects of knockdown of Atg5 or NPM1 on global ES gene expression of human Leukemia OCI-AML3 cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE69328 The effect of STARD3 knockdown on melanoma cell line MeWo
Contributors : Yuhui Huang ; Hirofumi TachibanaSeries Type : Expression profiling by arrayOrganism : Homo sapiensLittle is known about the role of STARD3 in melanoma. We performed microarrays to revealed the transcriptional change of a human melanoma cell line (MeWo) to scr-shRNA and STARD3-shRNA in order to provide insight into the role of STARD3 in MeWo cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE77089 Transcriptomic responses of Clostridium (Ruminiclostridium) thermocellum ATCC27405 and ethanol tolerant strains to ethanol stress
Contributors : Xiongjun Shao ; Babu Raman ; Courtney M Johnson ; Miguel Rodriguez ; Jonathan R Mielenz ; Lee R Lynd ; Steven D BrownSeries Type : Expression profiling by arrayOrganism : Ruminiclostridium thermocellum ATCC 27405Transcriptome profiles for Clostridium thermocellum ATCC 27405 wild type strain and two ethanol-adapted strains, E50A and E50C were generated to gain insights into ethanol tolerance. Details of the strains have been described, Shao X., et al. Appl Microbiol Biotechnol (2011) 92:641 –652. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Ruminiclostridium thermocellum ATCC 27405 Source Type: research

GSE77627 Whole genome profiling of liver biopsies discloses potential biomarkers for diagnosis of idiopathic non-cirrhotic portal hypertension
This study evaluates whether using new immunohistochemistry makers derived from whole genome analysis improves the diagnosis of INCPH. Methods. We analyzed formalin-fixed, paraffin embedded (FFPE) liver tissue from 18 INCPH and 22 patients with cirrhosis (LC) as well as from 14 histologically normal livers (HNL) as controls. Microarray experiments were performed using Illumina Whole-Genome DASL HT BeadChip arrays. Selected genes showing differential expression at Illumina were confirmed using quantitative real-time PCR (qRT-PCR) gene expression performed with Fluidigm Biomark HD system in a subgroup of samples. Immunohisto...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE79011 Transcriptome profile of rice genotypes IR24 and IRBB67 in interaction with Xanthomonas oryzae pv. oryzae under two temperature regimes
This study provides an understanding of how IRBB67 mediated resistance to Xoo under temperature get insight to cross talk in abiotic and biotic stress regulatory pathway. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Source Type: research

GSE81264 Comprehensive analysis of area-specific and time-dependent changes in gene expression in the motor cortex of macaque monkeys during recovery from spinal cord injury
Contributors : Toshio Kojima ; Noriyuki Higo ; Akira Sato ; Tatsuya Yamamoto ; Takao Oishi ; Yukio Nishimura ; Yumi Murata ; Hirotaka Onoe ; Tadashi IsaSeries Type : Expression profiling by arrayOrganism : Macaca mulattaThe present study aimed to assess the molecular bases of cortical compensatory mechanisms following spinal cord injury in primates. To accomplish this, comprehensive changes in gene expression were investigated in the bilateral primary motor cortex (M1), dorsal premotor cortex (PMd), and ventral premotor cortex (PMv) after a unilateral lesion of the lateral corticospinal tract (l-CST). At 2 weeks after the ...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Macaca mulatta Source Type: research

GSE88882 Gfi1b - A key player in genesis and maintenance of AML and MDS [expression microarray]
Contributors : Aniththa Thivakaran ; Lacra Botezatu ; Judith H önes ; Judith Schütte ; Lothar Vassen ; Nadine Olberding ; Yahya S Al-Matary ; Renata Köster ; Klaus Lennartz ; Andre Görgens ; Bernd Giebel ; Bertram Opalka ; Ulrich Dührsen ; Cyrus KhandanpourSeries Type : Expression profiling by arrayOrganism : Mus musculusDifferentiation of hematopoietic stem cells (HSCs) is regulated by a concert of different transcription factors (TFs). A disturbed function of TFs can be the basis of (pre)malignancies such as myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Growth Factor Independenc...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE88934 Gfi1b - A key player in genesis and maintenance of AML and MDS [ChIP-seq]
Contributors : Aniththa Thivakaran ; Lacra Botezatu ; Judith H önes ; Judith Schütte ; Lothar Vassen ; Nadine Olberding ; Yahya S Al-Matary ; Renata Köster ; Klaus Lennartz ; Andre Görgens ; Bernd Giebel ; Bertram Opalka ; Ulrich Dührsen ; Cyrus KhandanpourSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusDifferentiation of hematopoietic stem cells (HSCs) is regulated by a concert of different transcription factors (TFs). A disturbed function of TFs can be the basis of (pre)malignancies such as myelodysplastic syndrome (MDS) or acute myeloid leukem...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE88935 Gfi1b - A key player in genesis and maintenance of AML and MDS
Series Type : Expression profiling by array ; Genome binding/occupancy 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 - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE90007 Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression [methylation]
Contributors : Karla M O ’Neill ; Rachelle Irwin ; Sarah-Jayne Mackin ; Sara-Jayne Thursby ; Avinash Thakur ; Ciske Bertens ; Laura Masala ; Jayne Loughery ; Darragh McArt ; Colum P WalshSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensDNA methylation plays a vital role in the cell, but loss-of-function mutations of the maintenance methyltransferase DNMT1 in normal human cells are lethal, precluding target identification, and existing hypomorphic lines are tumour cells. We generated instead a hypomorphic series in normal hTERT-immortalised fibroblasts using stably integrated short hair...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE90011 Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression [expression]
Contributors : Karla M O ’Neill ; Rachelle Irwin ; Sarah-Jayne Mackin ; Sara-Jayne Thursby ; Avinash Thakur ; Ciske Bertens ; Laura Masala ; Jayne Loughery ; Darragh McArt ; Colum P WalshSeries Type : Expression profiling by arrayOrganism : Homo sapiensDNA methylation plays a vital role in the cell, but loss-of-function mutations of the maintenance methyltransferase DNMT1 in normal human cells are lethal, precluding target identification, and existing hypomorphic lines are tumour cells. We generated instead a hypomorphic series in normal hTERT-immortalised fibroblasts using stably integrated short hairpin RNA. Approx...
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE90012 Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression
Series Type : Expression profiling by array ; 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 - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE90965 Overexpression of 3 transcription factors uniquely induced by salt in Arabidopsis
Contributors : Ayan Sadhukhan ; Yuriko Kobayashi ; Hiroyuki KoyamaSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaOverexpression of ERF019, BBX29 and CCA1 in Arabidopsis (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE93362 Differential gene expression of M. tuberculosis in adipocytes and preadipocytes reveals redundancy of iron storage machinery in a fat rich host
Contributors : Ananya Nandy ; Anupam K Mondal ; Rajesh Pandey ; Prabhakar Aramugam ; Neetika Jaisinghani ; Vivek Rao ; Debasis Dash ; Sheetal GandotraSeries Type : Expression profiling by high throughput sequencingOrganism : Mycobacterium tuberculosis H37RvRNA-seq based discovery of physiologic state of M. tuberculosis in fat rich cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 31, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mycobacterium tuberculosis H37Rv Source Type: research