GSE112312 WGBS assessment of global methylation alterations in Dnmt3a1KO , Dnmt3a2KO, Dnmt3aKO, Tet1KO and DKO mouse embryonic stem cells
Contributors : Sean M Cullen ; Xueqiu Lin ; Wei Li ; Margaret A GoodellSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusUsing WGBS we assessed global DNA methylation changes in Dnmt3a1KO/Dnmt3a2KO/Dnmt3aKO/Tet1KO/DKO mouse embryonic stem cells. Compared with WT cells, Dnmt3aKO cells but not Dnmt3bKO cells showed genome-wide hypomethylation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE112948 Transcription factor IRF8 orchestrates the adaptive natural killer cell response
Contributors : Colleen M Lau ; Joseph C SunSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNatural killer (NK) cells are innate lymphocytes that have been recently appreciated to display features of adaptive immunity in response to viral infection. Biallelic mutations in the IRF8 gene have been reported to cause familial NK cell deficiency and susceptibility to severe viral infection in humans; however, the precise role of this transcription factor in regulating NK cell function remained unknown. Here, we show that IRF8 is required in a cell-intrinsic manner for NK cell-mediated prote...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114353 WTX overexpression effect on gastric cell line
Contributors : Q Zhang ; J Li ; D YeSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe used microarrays to detail the global gene expression in AGS gastric cancer cells overexpressing WTX, a tumor suppressor frequently inactivated in Wilms tumor. Results provide insight into roles for WTX in gastric cancer cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE114452 Differential roles of TAp63 α and deltaNp63α in chicken myogenic differentiation
Contributors : Wen Luo ; Xiquan ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallusWe constructed chicken TAp63 α and deltaNp63α overexpression vectors, and then transfected into chicken primary myoblast. After 48 hours transfection, we collected total RNA and conducted RNA-sequencing by using BGISEQ-500. GFP overexpression vector was used as control. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Gallus gallus Source Type: research

GSE114458 Transcriptomic analyses of gastrointestinal function in the “dwarf” and “medium” forms of Sthenoteuthis oualaniensis during sexual maturation
Contributors : Lulu Yan ; Chao Zhao ; Jun Zhang ; Lihua Qiu ; Zuozhi ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Sthenoteuthis oualaniensisSthenoteuthis oualaniensis (SA) is an important squid species in the South China Sea. Based on SA samples collected in 2016, SA was divided into the “dwarf” form (DF) and “medium” form (MF). To understand the changes in gastrointestinal function in SA during sexual maturation, we undertook transcriptomic analyses of the stomach and intestine tissues of the DF and MF of SA using the deep-sequencing platform Illumina HiSeq™....
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Sthenoteuthis oualaniensis Source Type: research

GSE114469 Expression data from NPY Y1R-deficient osteoblastic cells
Contributors : Nicola J Lee ; Herbert HerzogSeries Type : Expression profiling by arrayOrganism : Mus musculusNPY signalling via osteoblastic Y1 receptors has been shown to control bone mass but also contributes significantly to the control of whole-body insulin secretion and glucose homeostasis in mice through the release of novel factor(s) which are different from the previously implicated osteocalcin.We used microarrays to identify novel endocrine factors regulated by Y1 receptors and involved in the regulation of bone mass and whole-body homeostasis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE114478 Cis-regulatory divergence of eloF drives reproductive isolation in Drosophila
Contributors : Peter Combs ; Joshua Krupp ; Neil Khosla ; Dmitri Petrov ; Joel Levine ; Hunter FraserSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila sechellia x Drosophila simulansThe differential production of pheromones is a major barrier to mating between species in Drosophila. Individuals from morphologically similar sister species can produce different sets of cuticular hydrocarbons that allow potential mates to identify them as a suitable partner. In order to elucidate cis-regulatory mechanisms behind speciation, we looked for allele-specific expression in hydrocarbon-producing o...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila sechellia x Drosophila simulans Source Type: research

GSE114480 Rapid high-resolution measurement of DNA replication timing by droplet digital PCR
Contributors : Dzmitry G Batrakou ; Emma D Heron ; Conrad A NieduzhynskiSeries Type : OtherOrganism : Homo sapiensTime of DNA replication is inversely proportional to the relative DNA copy number. Sort-seq is a technique that uses deep short read sequencing to determine relative copy number across genome from sorted S phase cells. We have applied sort-seq to HeLa cells and report their relative copy number profile. The high (close to 2) value means the region replicates early in S phase; the low (close to 1) value means the region is replicated late in S phase. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE114482 Transcriptional profiles of miR-155 overexpressing CD8T cells during chronic infection
Contributors : ERIETTA STELEKATI ; E J WherrySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPersistent viral infections and tumors drive development of exhausted T (TEX) cells. In these settings, TEX cells establish an important host-pathogen or host-tumor stalemate. However, TEX cells erode over time, leading to loss of pathogen or cancer containment. We identified microRNA (miR)-155 as a key regulator of sustained TEX cell responses during chronic lymphocytic choriomeningitis virus (LCMV) infection. Genetic deficiency of miR-155 ablated CD8 T cell responses during chronic infection...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114489 Altered Cell-Cycle Control, Inflammation and Adhesion in High-Risk Persistent Bronchial Dysplasia
Contributor : Dan MerrickSeries Type : Expression profiling by arrayOrganism : Homo sapiensPersistent bronchial dysplasia (BD) is associated with increased risk of developing invasive squamous cell carcinoma (SCC) of the lung. We hypothesized that differences in gene expression profiles between persistent and regressive BD would identify cellular processes that underlie progression to SCC. RNA expression arrays (Affymetrix Hu 1.0) comparing baseline biopsies from 32 bronchial sites that persisted/progressed to 31 regressive sites showed 395 differentially expressed genes (ANOVA, FDR (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE114499 Unilateral mastication induced alternations of microRNAs expression profiling in synovium of rat temporomandibular joint
Contributors : Mengjie Wu ; Yiqun ZhouSeries Type : Non-coding RNA profiling by arrayOrganism : Rattus norvegicusThe present study investigated the alterations of miRNA expression profiling in synovium of temporomandibular joint(TMJ) in a rat model of experimental unilateral mastication. The synovium tissue of TMJ condyles from rats with 4- and 8-weeks unilateral mastication were harvested to extract miRNA for profiling holistic expression alternations. A total of 20 differentially expressed miRNAs were identified. Except for 3 miRNAs with uncertain function, those miRNAs are associated with cell proliferation, invasion, a...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Rattus norvegicus Source Type: research

GSE114501 Gene expression from mouse lung adenocarcinoma-associated macrophages
Contributors : Song Na-Young ; Hu YinlingSeries Type : Expression profiling by arrayOrganism : Mus musculusComparison of gene expression of mouse lung adenocarcinoma-associated macrophages isolated from C57BL/6 mice injected with Kras-CL and Kras IKKa low cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE114442 Comparison of oligodendrocyte miRNAs in normal and differentiated conditions in culture
Contributors : Yuki Miyamoto ; Junji YamauchiSeries Type : Non-coding RNA profiling by arrayOrganism : Rattus norvegicusOligodendrocyte miRNAs in normal and differentiated conditions are compared. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Rattus norvegicus Source Type: research

GSE94091 Cryptococcus neoformans sexual reproduction is controlled by a quorum sensing peptide
Contributors : Xiuyun Tian ; Guangjun He ; Pengjie Hu ; Lei Chen ; Changyu Tao ; Ying-Lu Cui ; Lan Shen ; Weixin Ke ; Haijiao Xu ; Youbao Zhao ; Qijiang Xu ; Fengyan Bai ; Bian Wu ; Ence Yang ; Xiaorong Lin ; Linqi WangSeries Type : Expression profiling by high throughput sequencingOrganism : Cryptococcus neoformans var. neoformansMating pheromone is the best-known fungal paracrine signal whose essentiality in determining sexual reproduction has been recognized since six decades ago. We demonstrate that the pheromone cannot induce mating response during unisexual mating due to the lack of a compatible receptor from the sam...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Cryptococcus neoformans var. neoformans Source Type: research

GSE98899 A systems biology approach in understanding oncogenic cooperation between TAL1 expression and PTEN deletion in T-cell acute lymphoblastic leukaemia
Contributors : Simon Bornschein ; Sofie Demeyer ; Rocco Stirparo ; Olga Gielen ; Ellen Geerdens ; Bart Ghesquiere ; Stein Aerts ; Jan Cools ; Charles E de BockSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusT-cell acute lymphoblastic leukemia (T-ALL) is caused by the accumulation of multiple mutations combined with the ectopic expression of transcription factors. However, how these transcription factors cooperate with oncogenic mutations has been difficult to assess due to a lack of robust T cell model systems. Here we utilize a new ex vivo pro-T cell model to study oncogenic cooperat...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE98975 Genome-wide maps of MBD1 in mouse dentate gyrus
We report the MBD1 binding profiles in mouse dentate gyrus by sequencing MBD1 chromatin immunoprecipitated DNA (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE99000 Genome-wide profiling of active regulatory elements in dentate gyrus of WT and MBD1 KO mice
We report the genome-wide active regulatory elements in mouse dentate gyrus with or without presence of MBD1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE99001 MBD1 activates neuronal developmental genes through modulating chromatin structure during neuronal maturation
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 - May 15, 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

GSE99171 Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [ChIP-seq]
This study reveals crucial functions of BET proteins and provides the rationale and therapeutic merits of targeted degradation of BET proteins by dBET6 in GBM. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE99175 Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [RNA-seq]
This study reveals crucial functions of BET proteins and provides the rationale and therapeutic merits of targeted degradation of BET proteins by dBET6 in GBM. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE99181 Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [RNA-seq (time course)
This study reveals crucial functions of BET proteins and provides the rationale and therapeutic merits of targeted degradation of BET proteins by dBET6 in GBM. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE99183 Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy NA-seq (time course) May 15, 2018 approved TSV
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy 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 - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE102284 RNA-Seq transcriptome profiling of soleus from adult and aged mice following disuse muscle atrophy and recovery
We report the application of Next-generation sequencing (NGS) technology for high-throughput profiling of mRNA in soleus muscle of adult (6 mo) and aged (22-24 mo) mice. Our goal was to determine the effects of hind limb unloading and r eloading on mRNA profiles in soleus muscle and compare between adult and aged mice. We find that there are distinct response in the profile of fatty acid oxidation, TCA cycle, ETC oxidative phosphorylation gene expression patterns in response to unloading and reloading. The repsonses are generally s imialr between young and old mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE106932 Neuropilin-1 is Required for the Suppressive Function of Human Regulatory T Cells
Contributors : Kate Milward ; Joanna Hester ; Ruud van StiphoutSeries Type : Expression profiling by arrayOrganism : Homo sapiensRegulatory T cells (Tregs), lymphocytes that suppress immunological reactions, are of great interest for our comprehension of homeostasis and regulation in the immune system and as a therapeutic target in the treatment of both immune-mediated pathologies and reactivation of the immune response in patients with cancer. Understanding the molecular mechanisms by which these cells are regulated in respone to their environment will help to inform clinical strategies targeting Tregs. We hypothesised th...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE107004 Transcriptomic analysis of adult mouse hippocampal tissue in control and MeCP2 knockdown conditions
We report gene expression data of mouse adult hippocampal tissue in which MeCP2 has been knockeddown in both conditions. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE107064 Liver transcriptomic and plasma metabolic profile of fattening lambs is modified by feed restriction during the suckling period.
Contributors : Alba Santos ; Francisco J Gir áldez ; Erminio Trevisi ; Luigi Lucini ; Javier Frutos ; Sonia AndrésSeries Type : Expression profiling by high throughput sequencingOrganism : Ovis ariesPurpose: The present study was designed to identify both differentially expressed (DE) genes in the liver tissues of fattening Merino lambs and differences in metabolites accumulated in plasma, thus trying to identify modified metabolic pathways as a consequence of milk restriction during the suckling period.Methods: Twenty-four male Merino lambs were assigned to 2 different groups (n=12 per dietary treatment). Th...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Ovis aries Source Type: research

GSE107199 Next Generation Sequencing for Quantitative Transcriptomic Profiling of TLR3, TLR7 and TLR8 Activation in Neurons
Contributors : Yun-Fen Hung ; Chiung-Ya Chen ; Yi-Ping HsuehSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study is to compare gene expression of mouse cultured cortical and hippocampal neurons in response to TLR3, TLR7 and TLR8 activation (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111525 Expression of small RNAs during epigenetic disturbances of Tetrahymena DNA elimination
In this study, we test the existence of such small RNA-mediated communication by epigenetically disturbing the pattern of DNA elimination in Tetrahymena. We show that the pattern of DNA elimination is indeed determined by the selective turnover of small RNAs, which is induced by the interaction between germline-derived small RNAs and the somatic genome. In addition, we show that DNA elimination of an element is regulated by small RNA-mediated communication with other eliminated elements. By contrast, no evidence obtained thus far supports the notion that transfer of epigenetic information from the soma to the germline, if ...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Tetrahymena thermophila Source Type: research

GSE111528 Tissue damage signaling is essential for protective neutrophil recruitment to microbial infection in zebrafish (Danio rerio)
Contributors : C Huang ; P NiethammerSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioRNAseq was performed on zebrafish larvae infected with bacteria under different osmotic pressures. The trascriptome profile generated here reveals the differential immune gene expression pattern. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE111949 Differential expression analysis from MV4-11 cells treated with or without APTO-253 for 6 hours.
Contributors : Hannah Zhang ; Andrea LocalSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq and differential gene expression analysis were used to detect specific genes and pathways either up or down regulated in the AML cell line MV4-11 after treatment with novel small molecule APTO-253. The aim of the analysis was to elucidate genes or pathways that are key to the celular phenotype of APTO-253 mechanism of action in killing AML cells. W detected an effect on MYCexpression, DNA damage and cell stress response pathwyas and cell cycle arrest. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112395 Myc and the Tip60 chromatin remodeling complex control neuroblast maintenance and polarity in Drosophila
Contributor : Andreas WodarzSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterTranscriptomic analyses of wild type and Domino knockdown 3rd instar larval neural cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE112588 Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
In this study, we analyzed the genome-wide epigenetic and transcriptional patterns of the white-rot basidiomycete Pleurotus ostreatus throughout its life cycle. Our results performed by using high-throughput sequencing analyses revealed that strain-specific DNA methylation profiles are primarily involved in the repression of transposon activity, and suggest that 21 nt small RNAs play a key role in transposon silencing.Furthermore, we provide evidence that transposon-associated DNA methylation, but not sRNA production, is directly involved in the silencing of genes surrounded by transposons. Finally, we identified key genes...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Pleurotus ostreatus Source Type: research

GSE114378 Novel human full-thickness, three-dimensional non-keratinized mucous membrane model for pharmacological studies in wound healing
Contributors : Laurenz Schmitt ; Yvonne Marquardt ; Ruth Heise ; Verena von Felbert ; Philipp M Amann ; Timm Steiner ; Frank H ölzle ; Sebastian Huth ; Jens M BaronSeries Type : Expression profiling by arrayOrganism : Homo sapiensEfforts are increasingly aiming to develop in vitro models that can provide effective alternatives to in vivo experiments. The main aim of this study was the establishment of an in vitro model of the non-keratinized mucous membrane that can be used as a standardized tool to evaluate biological and therapeutic effects of pharmaceuticals for mucosal wound healing. Performing histological and im...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE114384 Expression data of sheep exposed to Mycobacterium avium subsp. Paratuberculosis
In this study, consistent gene expression changes were analysed to identify gene-to-gene interaction and functional pathway relationships associated with the MAP exposure outcomes of either a paucibacillary or a multibacillary disease form or sheep resilient to disease. The results suggest that although groups of genes are differentially changed in the MAP exposed sheep regardless of clinical outcome, there are distinct variations in gene expression patterns between the paucibacillary and multibacillary forms of disease and of particular note was the finding that MAP exposed animals with evidence of recovery or resilience ...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Bos taurus Ovis aries Source Type: research

GSE114385 A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer
Contributors : Xintao Qiu ; David Y Takeda ; Sandor Spisak ; Matt L FreedmanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensIncreased androgen receptor (AR) activity drives therapeutic resistance in advanced prostate cancer. The most common resistance mechanism is amplification of this locus presumably targeting the AR gene. Here, we identify and characterize a somatically acquired AR enhancer located 650 kilobases centromeric to the AR. Systematic perturbation of this enhancer using genome editing decreased proliferation by suppressing AR levels. Insertion of an additio...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114390 Hsa-miR99b/let-7e/miR125a cluster regulates pathogen recognition receptor-stimulated suppressive APCs
Contributors : Dagmar Hildebrand ; Mariel E Eberle ; Sabine W ölfe ; Franziska Egler ; Delal Sahin ; Aline Sähr ; Konrad A Bode ; Klaus HeegSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensAntigen presenting cells (APCs) regulate the balance of our immune response towards microbes. Whereas immunogenic APCs boost inflammation and activate lymphocytes, the highly plastic cells can switch into a tolerogenic/suppressive phenotype that dampens and resolves the response. Thereby the initially mediated inflammation seems to prime the switch of APCs while the strength of activation determines the gra...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE114397 Single cell RNA-seq and ATAC-seq of EMT induced by TGFbeta stimulation and Zeb1 overexpression
We report the application of single cell RNA-sequencing using indrop on an HMLE breast cancer cell line that we induced to undergo EMT. We measured 7523 single cells after 8 and 10 days of stimulation with TGFbeta. In addition, we measured 3496 single cells in an engineered HMLE cell line with Dox inducible Zeb1, after 2 days of stimulation with Doxycycline. Finally, we performed ATAC-seq on CD44 sorted HMLE cells after 8 days of stimulation with TGFbeta. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114426 Circular RNA expression alteration in rats after traumatic spinal cord injury (SCI)
Contributors : Chuan Qin ; Jian-Jun LiSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusTo determine whether the expression levels of circular RNAs were altered and lay a foundation for future work, we used high-throughput microarray analysis to screen circular RNAs expression patterns in the spinal cord of adult rats after traumatic spinal cord injury (SCI), finally to evaluate the potential rat models as a platform for the development of novel therapeutic targets for spinal cord injury in future clinical studies. Overall six rats at 3 days post-SCI in two groups were used to perform the microarray. (...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE114428 Genome-wilde expression profiling analysis of yeast cells lacking the decapping activator Scd6
Contributors : Feng He ; Allan JacobsonSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeTo assess the role of the decapping activator Scd6 in mRNA decay, we used RNA-Seq to analyze the expression profile of yeast cells harboring a deletion of the SCD6 gene. Consistent with our recent model for decapping regulation, we found that Scd6 targets a small number of specific mRNAs in yeast cells. Interestingly, degradation of Scd6-targeted transcripts also requires the functions of the decapping activators Pat1, Lsm1, and Dhh1, suggesting that Scd6 functions together with Pat1, Ls...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE114431 Pseudomonas aerugiosa tctED deletion strain compared to wildtype
Contributors : Patrick K Taylor ; Thien-Fah MahSeries Type : Expression profiling by arrayOrganism : Pseudomonas aeruginosa ; Pseudomonas aeruginosa UCBPP-PA14Purpose of study was to investigate whole genome expression changes of a strain with deletion of the two-component system TctD-TctE and determine genes dysregulate relative to the parental wildtype to gain insight into possible regulatory targets of TctD-TctE.TctD-TctE is a two-component system in Pseudomonas aeruginosa that responds to and regulates uptake of tricarboxylic acids such as citric acid. It accomplishes this through derepression of the porin encoding the...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Pseudomonas aeruginosa Pseudomonas aeruginosa UCBPP-PA14 Source Type: research

GSE114434 Tissue-resident macrophages in the intestine are long-lived and defined by Tim-4 and CD4 expression
Contributors : Tovah N Shaw ; Stephanie A Houston ; Kelly Wemyss ; Hayley M Bridgeman ; Thomas A Barbera ; Tamsin Zangerle-Murray ; Patrick Strangward ; Amanda J Ridley ; Ping Wang ; Samira Tamoutounour ; Judith E Allen ; Joanne E Konkel ; John R GraingerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusA defining feature of resident gut macrophages is their high replenishment rate from blood monocytes, attributed to tonic commensal-stimulation of this site. In contrast, almost all other tissues contain locally maintained macrophage populations, which co-exist with monocyte-replenished ...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114435 Determining ELL2 direct targets via ChIPseq
Contributors : Christine Milcarek ; Ashley M NelsonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusA plasma cell line was used to determine which genes have ELL2 protein bound to them. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE114438 A PDGFR α-driven mouse model of Glioblastoma reveals a Stathmin1-mediated mechanism of sensitivity to Vinblastine
Contributors : Hyun-Jung Jun ; Al CharestSeries Type : Expression profiling by arrayOrganism : Mus musculusGlioblastoma multiforme (GBM) is an aggressive primary brain cancer that includes focal amplification of PDGFR α and for which there are no effective therapies. Herein, we report the development of a genetically engineered mouse model of GBM based on autocrine, chronic stimulation of PDGFRα and the analysis of GBM signaling pathways using proteomics. We discovered the tubulin-binding protein Stathmin1 (STM N1) as a PDGFRα phospho-regulated target and that this mis-regulation conferred selective sensi...
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE114441 Schwann cell precursor mRNA in normal culture conditions
Contributors : Yuki Miyamoto ; Junji YamauchiSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusSchwann cell precursor mRNA are carried out in RNAome analyses (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE113112 TCR repertoire of effector CCR7-CD38+ cells accumulating during experimental infection with Typhoidal Salmonella
Contributors : Margarida Rei ; David Miguel Susano Pinto ; Giorgio NapolitaniSeries Type : OtherOrganism : Homo sapiensIn order to characterize pathogen specific T cell responses against Salmonella volunteers challenged with Salmonella enterica serovar Typhi (S. Typhi) or Salmonella Paratyphi A (S. Paratyphi). we used mass cytometry, to identify effector CD4+ T cells circulating during infection. We identified a population of CCR7-CD38+ cells accumulating during infection, and via unbiased single cell cloning and expansion we demonstrated that these CCR7-CD38+ cells are enriched in Salmonella specific T cells. In this expe...
Source: GEO: Gene Expression Omnibus - May 13, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE107627 RNA sequence reveal gene expression mechanism of sugar beet in response to alkaline stress
Contributors : Chunlei Zou ; Caifeng LiSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Beta vulgarisHere, we first systematically identified and characterized responsive lncRNAs and mRNAs expressed in leaves of sugar beet at a genome-wide scale, focusing on alkaline-responsive lncRNAs and mRNAs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Beta vulgaris Source Type: research

GSE114369 Transcriptomic analysis on leaves of C. sinensis under low-pH
Conclusion:The inhibition of the seedling growth in low pH may be related to the differentially expression of genes in glycometabolism, amino acid metabolism, protein metabolism, carbon fixation in photosynthetic organisms, chloroplast component, porphyrin and chlorophyll metabolism and plant hormone signal transduction. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 12, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Citrus sinensis Source Type: research

GSE57636 Gene expression profiling of mouse small intestinal myofibroblast after stimulation with homogenate of intestinal eosinophil
Contributors : Naoki Takemura ; Satoshi UematsuSeries Type : Expression profiling by arrayOrganism :GeneChip ® Mouse Gene 2.0 ST Array was used to comprehensively investigate the changes of gene expression of small intestinal myofibroblasts of mice after stimulation with homogenates of intestinal eosinophils in vitro. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 12, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Source Type: research

GSE112178 Molecular characterization of pyrethroid resistance in the olive fruit fly Bactrocera oleae
Contributors : Nena Pavlidi ; Anastasia Kampouraki ; Vasilis Tseliou ; Nicky Wybouw ; Wannes Dermauw ; Emmanouil Roditakis ; Ralf Nauen ; Thomas van Leeuwen ; John VontasSeries Type : Expression profiling by arrayOrganism : Bactrocera oleaeΑ reduction of pyrethroid efficacy has been recently recorded in the olive fruit fly Bactrocera oleae, the most destructive insect pest of olives worldwide.We analyzed the transcriptomic differences between two highly pyrethroid resistant populations versus a relatively susceptible field population and two laboratory strains to gain more insight into the molecular mechanism of resi...
Source: GEO: Gene Expression Omnibus - May 12, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Bactrocera oleae Source Type: research

GSE114262 RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature
Contributors : Yuzhi Hong ; Xilin ZhaoSeries Type : Expression profiling by high throughput sequencingOrganism : Escherichia coliTo generate a bona fide model to study post-stress baterial programmed cell death (PCD), we used a temperature-sensitive E. coli mutant (dnaB-Ts) since temperature stress can be rapidly reversed while other stress, such as antibotic treatment, is difficult to be rapidly and completely stopped and removed for post-stress PCD analysis. When cells were shifted from permissive (30 °C) to non-permissive temperature (42 °C), the dnaB-Ts ΔahpC double mutant maintained full surival while su...
Source: GEO: Gene Expression Omnibus - May 12, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Escherichia coli Source Type: research