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GSE106568 Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ibm1-3 trancriptomes in normal light and high light condition
This study could con tribute to a better understanding of the linkage between light signaling and anthocyanin biosynthesis in plants (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE106591 Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and miR-211-/- Whole Eye Transcriptomes
Contributors : Ivan Conte ; Sandro Banfi ; Sara BarbatoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS transcriptome profiling (RNA-seq) from whole eye, after removal of the lens and cornea from 1-2 month old miR-211-/- mice and compare it with wt miceMethods: Whole eye (after removal of the lens and cornea) mRNA profiles of 1-2 month old wild-type (WT) and neural miR-211-/-mice were generated by deep sequencing, in multiple biological re...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE106603 Gene expression data of PFKFB3 KD in SMMC7721 cell line
In this study, we found that PFKFB3 expression is associated with hepatocellular carcinoma (HCC) growth and mainly located in the nucleus of tumor cells. PFKFB3 overexpression was associated with large tumor size, and poor survival of patients with HCC. Knockdown of PFKFB3 inhibited HCC growth, not only by reducing glucose consuming but also damaging DNA repair function leading to G2/M phase arrest and apoptosis. Therefore, we performed a cDNA microarray in PFKFB3 knockdown SMMC7721 cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE106619 Functional involvement of microRNAs in T cell ageing-related decline of CD28 expression
Contributors : Nato Teteloshvili ; Gerjan Dekkema ; Peter Heeringa ; Pytrick Jellema ; Debora de Jong ; Martijn Terpstra ; Elisabeth Brouwer ; Graham Pawelec ; Annemieke Boots ; Klaas Kok ; Anke van den Berg ; Joost Kluiver ; Bart-Jan KroesenSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensMicroRNA expression profiling of T-cell clones with high or low population doublings as a longitudinal model of age-associated gene expression changes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106776 Differential miRNA profiles in cumulus and mural granulosa cells from human pre-ovulatory follicles
Contributors : Daniela Andrei ; Ruxandra Nagy ; Aafke van Montfoort ; Uwe Tietge ; Martijn Terpstra ; Klaas Kok ; Anke van der Berg ; Annemieke Hoek ; Joost Kluiver ; Rogier DonkerSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensSmall RNA seq analysis identified several hundreds of miRNAs being expressed in MGC and CC. 53 miRNAs were differentially regulated (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106845 MAP kinase-dependent cell-to-cell movement drives plant tissue invasion by the rice blast fungus
Contributors : Wasin Sakulkoo ; Miriam Os és-Ruiz ; Ely O Garcia ; Darren M Soanes ; George R Littlejohn ; Christian Hacker ; Ana Correia ; Barbara Valent ; Nicholas J TalbotSeries Type : Expression profiling by high throughput sequencingOrganism : Magnaporthe oryzaeWe created a mutant in the MAP kinase-encoding Pmk1 gene of the rice blast fungus Magnaporthe oryzae (pmk1AS) that renders the gene sensitive to inhibition by 1NA-PP1. Fungal gene expression was compared during infection of rice sheath by the M. oryzae pmk1AS mutant in the presence and absence of 1NA-PP1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Magnaporthe oryzae Source Type: research

GSE106849 CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9
This study investigates the RNA targets and cleavage sites of endogenous Cas9 in the food-borne pathogen Campylobacter jejuni. Direct RNA binding targets of Cas9 in C. jejuni strain NCTC11168 were determined using RIP-seq. The Cleavage sites were then predicted in the RNA targets by comparing total transcriptome data from WT and deletion (cas9, crRNA3, tracrRNA, CRISPR-tracrRNA) strains. PAMs for the CjeCas9 were enriched using the PAM-SCANR platform, which operates through a GFP reporter gene. Upon GFP (and thus functional PAM) enrichment, fluorescing cells were isolated using FACS and prepared plasmid DNA was amplified a...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Campylobacter jejuni Escherichia coli K-12 Source Type: research

GSE106883 Impact of bariatric surgery on placental transcriptome
Contributor : Bernadette GraysonSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusIn the present study, we sought to understand the impact of bariatric surgery [using vertical sleeve gastrectomy (VSG)] on transcriptome changes in the placenta . Female Adult, Long Evans were fed high fat diet (HFD, #D03082706, Research Diets) for 4 weeks, divided into sham-VSG or VSG groups, and following surgeries one group of sham-VSG and VSG were switched to normal diet (lean), while one sham-VSG group (obese) continued HFD. At gestdational day 18, placenta tissues harvested from pregnant female rats were processed f...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE106935 5hmC-seq in human kidney DNA
Contributors : John P Thomson ; Angie FawkesSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensDNA IP for 5hmC modified CpGs to determine 5hmC paterns across male human kidney (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107356 RNA-Sequencing of Running-dependent and Running-independent Environmental Enrichment in the Adult Mouse Dentate Gyrus
Contributors : Catherine-Alexandra Gr égoire ; Karl J FernandesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe used RNA sequencing to perform an unbiased interrogation of DG gene expression in CD1 mice exposed to either a voluntary running disc (RUN), a running-independent complex environment (CE, containing a locked disc, social enrichment and tunnels), or a locked disc alone (LD). RNA sequencing revealed that both RUN and CE mice showed significant, and largely non-overlapping, transcriptomic differences versus the LD control. Our findings reveal stimulus-dependent transcr...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE107371 Hierarchical roles of mitochondrial PAPI and Zucchini in Bombyx germline piRNA biogenesis
Contributors : Kazumichi M Nishida ; Kazuhiro Sakakibara ; Mikiko C SiomiSeries Type : Other ; Non-coding RNA profiling by high throughput sequencingOrganism : Bombyx moriPIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity1,2,3. To achieve this, piRNAs bind PIWI proteins upon being processed from piRNA precursors1,2,3. Bioinformatic studies of piRNA biogenesis in Drosophila showed that the piRNA 5 ′ end is formed by PIWI-Slicer or Zucchini (Zuc) endonucleolytic cleavage, while the 3′ end is formed by Zuc or Nibbler (Nbr) 3′-to-5′ exon...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Other Non-coding RNA profiling by high throughput sequencing Bombyx mori Source Type: research

GSE107472 Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [RNA-Seq]
Contributors : Shasha Li ; Shuaishuai Teng ; Dong WangSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensCircular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. The numbers of up- and down-regulated circRNAs during tumorigene...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107691 Expression data from Wild-type (WT) and Astrocyte elevated gene-1 (AEG-1) knockout (KO) bone marrow derived macrophages (BMDM)
Contributors : Devanand Sarkar ; Mikhail DozmorovSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAEG-1 is overexpressed in human hepatocellular carcinoma (HCC) and positively regulates inflammation and development and progression of HCC. An AEG-1KO mouse was generated to understand the function of AEG-1 in inflammatory processes in HCC. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE107883 Functional analysis of HD2C in Arabidopsis
Contributors : Li Lu ; Xiangsong Chen ; Xuehua ZhongSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Arabidopsis thalianaRibosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis histone deacetylase HD2C in pre-rRNA processing via bot...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Arabidopsis thaliana Source Type: research

GSE108077 Temperature-dependent Reprogramming of Beige Adipocyte Identity
Contributors : Roh Hyun ; Rosen EvanSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusBeige and brown adipocytes generate heat in response to reductions in ambient temperature. When warmed, both beige and brown adipocytes exhibit morphological ‘whitening’, but it is unknown whether or to what extent this represents a true shift in cellular identity. Using cell type-specific profiling in vivo, we uncover a unique paradigm of temperature-dependent epigenomic plasticity of beige, but not brown, adipocytes, with ...
Source: GEO: Gene Expression Omnibus - March 1, 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

GSE108085 Comprehensive molecular profiling of children with recurrent cancer I
Contributors : Olga Østrup ; Karsten Nysom ; David Scheie ; Ane Y Schmidt ; Rene Mathiasen ; Lisa L Hjalgrim ; Tina E Olsen ; Jane Skjøth-Rasmussen ; Birthe M Henriksen ; Finn C Nielsen ; Peder S Wehner ; Henrik Schrøder ; Astrid Sehested ; Catherine Rechnitzer ; Maria RossingSeries Type : Genome variation profiling by SNP array ; SNP genotyping by SNP arrayOrganism : Homo sapiensto explore possible treatment targets and reasons for agressive children cacners by comprehensive molecular profiling on several platformsto explore copy number aberrations related to cancers (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array SNP genotyping by SNP array Homo sapiens Source Type: research

GSE108088 Comprehensive molecular profiling of children with recurrent cancer II
Contributors : Olga Østrup ; Karsten Nysom ; David Scheie ; Ane Y Schmidt ; Rene Mathiasen ; Lisa L Hjalgrim ; Tina E Olsen ; Jane Skjøth-Rasmussen ; Birthe M Henriksen ; Finn C Nielsen ; Peder S Wehner ; Henrik Schrøder ; Astrid Sehested ; Catherine Rechnitzer ; Maria RossingSeries Type : Expression profiling by arrayOrganism : Homo sapiensto explore possible treatment targets and reasons for agressive children cacners by comprehensive molecular profiling on several platformsto explore copy number aberrations related to cancers (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE108089 Comprehensive molecular profiling of children with recurrent cancer
Series Type : Expression profiling by array ; Genome variation profiling by SNP array ; SNP genotyping by SNP arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Genome variation profiling by SNP array SNP genotyping by SNP array Homo sapiens Source Type: research

GSE108176 The embryo affects day 14 uterine transcriptome depending on the nutritional status in sheep
Contributors : Victoria de Brun ; Juan J Loor ; Mario Vailati-Riboni ; Omar Bulgari ; Khuram Shahzad ; Jos é A Abecia ; Cecilia Sosa ; Ana MeikleSeries Type : Expression profiling by arrayOrganism : Ovis ariesTranscriptomics and functional bioinformatics were used to investigate the potential interactions of undernutrition and the presence of the conceptus at the time of maternal recognition of pregnancy on uterine indicators of metabolism and reproduction. Adult Rasa Aragonesa ewes were allocated to one of two planes of nutrition during 28 days: maintenance energy intake (control; 5 cyclic, 6 pregnant ewes) providi...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Ovis aries Source Type: research

GSE108203 Tumor evolution in the context of castration resistance in prostate cancer
Contributors : Jo ël R Federer-Gsponer ; Cristina Quintavalle ; David C Müller ; Tanja Dietsche ; Valeria Perrina ; Thomas Lorber ; Darius Juskevicius ; Elisabeth Lenkiewicz ; Tobias Zellweger ; Thomas Gasser ; Michael T Barrett ; Cyrill A Rentsch ; Lukas Bubendorf ; Christian RuizSeries Type : Genome variation profiling by arrayOrganism : Homo sapiensClinical resection specimens of prostate tissue (radical prostatectomy and TUR-P) over the course of hormone deprivation therapy were flow sorted according to their DNA content (Ploidy) and subjected to aCGH analysis to identify possiple chromosomal abberations whic...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by array Homo sapiens Source Type: research

GSE108252 Beta-catenin maintains lung epithelial progenitors after lung specification
Contributors : Edwin J Ostrin ; Jichao ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed RNA-seq on human embryonic stem cells raised in an established condition to produce 95% Nkx2.1 cells, with and without withdrawal of Wnt-agonist CHIR99021 or addition of Wnt-inhibitor IWP2 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108426 Transgenerational DNA methylation changes in Daphnia magna exposed to chronic gamma radiation
Contributors : Olivier Armant ; Marie Trijau ; Frederique AlonzoSeries Type : Methylation profiling by high throughput sequencingOrganism : Daphnia magnaDNA methylation epigenetic changes were analysed in Daphnia magna exposed for 25-day to chronic gamma irradiation compared to unexposed controls. Generation F0 were exposed to 6.5 μGy/h or 41.3 mG/h and let recoverd until the F3 generation without exposures to ionizing radiations. DNA-methylation patterns were analysed by WGBS on the whole organismes at the generation F0, F2 and F3 in order to detect possible transmission of DNA methylation changes to the progeny. (Sour...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Daphnia magna Source Type: research

GSE108447 AMPK promotes survival of c-Myc positive melanoma cells by suppressing oxidative stress
Contributors : Alain Kfoury ; Freddy Radtke ; Marion LeleuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAlthough c-Myc is essential for melanocyte development, its role in cutaneous melanoma, the most aggressive skin cancer, is only partly understood. Here we used the NrasQ61KINK4a-/- mouse melanoma model to show that c-Myc is essential for tumor initiation, maintenance and metastasis. c-Myc expressing melanoma cells were preferentially found at metastatic sites, correlated with increased tumor aggressiveness and high tumor initiation potential. Abrogation of c-Myc caused apoptosis ...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE108732 RNASeq libraries of quorum-sensing induced and wild-type M. ciceri bv. biserrulae WSM1271
Contributors : Timothy L Haskett ; Jason Terpolilli ; Vinoy Ramachandran ; Joshua RamsaySeries Type : Expression profiling by high throughput sequencingOrganism : Mesorhizobium ciceri biovar biserrulae WSM1271M. ciceri WSM1271 carries a novel integrative and conjugative element (ICE) termed a tripartite ICE (ICE3) that exists as thee separated DNA regions in the chromosome. Three site-specific recombinases acting on three distinct pairs of attachment sites catalyse recombination between the three ICE3 DNA regions leading to their excision from the chromosome to form a single plasmid-like entity for horizontal conjugative t...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mesorhizobium ciceri biovar biserrulae WSM1271 Source Type: research

GSE108759 ERCC TAC-seq
Contributors : Kaarel Krjutshkov ; Priit PaluojaSeries Type : OtherOrganism : synthetic constructTargeted assay to detect 22 selected ERCC spike-in mRNA molecules for method sensitivity testing purposes (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Other synthetic construct Source Type: research

GSE108831 Gene expression changes in Cenococcum geophilum 1.58-Populus tremulaxalba INRA 717-1B4 ectomycorrhizal roots compared to Cenococcum geophilum free-living mycelium
Contributors : Maira de Freitas Pereira ; Vasanth Singan ; Martina Peter ; Annegret Kohler ; Francis Martin ; Igor GrigorievSeries Type : Expression profiling by high throughput sequencingOrganism : Cenococcum geophilum 1.58Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal poplar roots compared to free-living mycelium . Ectomycorrhizal poplar roots and control mycelium were harvested after 60 days and used for RNA extraction. Reads of 150bp were generated and aligned to the C. geophilum reference genome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html). (Source: GEO: ...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Cenococcum geophilum 1.58 Source Type: research

GSE108841 Low-coverage TAC-seq expression in endometrium
Contributors : Kaarel Krjutskov ; Mariann Koel ; Priit PaluojaSeries Type : OtherOrganism : Homo sapiensTranscriptomic biomarker detection assay for targeted 57 human uterus endometrium receptivity testing with TAC-seq (targeted allele counting by sequencing). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE108866 Gene expression changes in Cenococcum geophilum 1.58-Pinus sylvestris ectomycorrhizal roots, sclerotia and extramatrical mycelium compared to Cenococcum geophilum free-living mycelium
Contributors : Maira de Freitas Pereira ; Vasanth Singan ; Martina Peter ; Annegret Kohler ; Francis Martin ; Igor GrigorievSeries Type : Expression profiling by high throughput sequencingOrganism : Cenococcum geophilum 1.58 ; Pinus sylvestrisIllumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal Pine roots, sclerotia and extramatrical mycelium compared to free-living mycelium . Ectomycorrhizal pine roots, sclerotia, extramatrical mycelium and control mycelium were harvested after 90 days and used for RNA extraction. Reads of 150bp were generated and aligned to the C. geophil...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Cenococcum geophilum 1.58 Pinus sylvestris Source Type: research

GSE108899 Genome-wide maps of H3K27me3 in endpoint Ezh2+/+ or Ezh2-/- Tet ON PyVmT mouse mammary gland tumours
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in endpoint tumours from Ezh2+/+ or Ezh2-/- Tet ON PyVmT mammary gland tumours. In order to understand the H3K27me3 targets in the context of mouse mamamry gland tumorigenesis, data were generated by deep sequencing a pool of 5 tumours per genoype, in duplicate using Illumina HiSeq2500. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10). Raw reads were trimmed for length (n>=32), quality (phred score>= 30) and adap...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE108916 Targeted microRNA-sequencing for precise biomarker molecule counting
This study introduced a novel targeted allele counting by sequencing (TAC-seq) method to quantify miRNA molecules. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE108926 The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma [ChIP-seq]
Contributors : Ana Banito ; Scott W LoweSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGene fusions arising from chromosomal translocations are key oncogenic drivers in soft tissue sarcomas but little is known about how they exert their oncogenic effects. Our study explores the molecular mechanisms by which the SS18-SSX fusion oncoprotein subverts epigenetic mechanisms of gene regulation to drive synovial sarcoma. Using functional genomics, we identify KDM2B – a histone demethylase and core component of a non-canonical Polycomb Repressive Complex 1 (PRC1.1) &ndash...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108927 The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma [ATAC-seq]
Contributors : Ana Banito ; Scott W LoweSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGene fusions arising from chromosomal translocations are key oncogenic drivers in soft tissue sarcomas but little is known about how they exert their oncogenic effects. Our study explores the molecular mechanisms by which the SS18-SSX fusion oncoprotein subverts epigenetic mechanisms of gene regulation to drive synovial sarcoma. Using functional genomics, we identify KDM2B – a histone demethylase and core component of a non-canonical Polycomb Repressive Complex 1 (PRC1.1) &ndash...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108928 The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma [RNA-seq]
Contributors : Ana Banito ; Scott W LoweSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGene fusions arising from chromosomal translocations are key oncogenic drivers in soft tissue sarcomas but little is known about how they exert their oncogenic effects. Our study explores the molecular mechanisms by which the SS18-SSX fusion oncoprotein subverts epigenetic mechanisms of gene regulation to drive synovial sarcoma. Using functional genomics, we identify KDM2B – a histone demethylase and core component of a non-canonical Polycomb Repressive Complex 1 (PRC1.1) – as selective...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108929 The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; 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 - March 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109009 Effect of GMG-43-AC on hair follicles
In this study, we aimed to explore the effects of PPARγ-stimulation in organ cultured human hair follicles. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE109053 MicroRNA markers of human endometrial receptivity
Contributors : Agne Velthut-Meikas ; Kaarel Krjutskov ; Andres SalumetsSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensThe goal of the study was to compare the miRNA profile of pre-receptive and receptive endometrium collected from women from the same menstrual cycle. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109124 Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39PcpsT= > C in medium without uracil
Contributor : Tomas G KloostermanSeries Type : Expression profiling by arrayOrganism : Streptococcus pneumoniae ; Streptococcus pneumoniae D39Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39PcpsT=>C in medium without uracil.Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae' (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Streptococcus pneumoniae Streptococcus pneumoniae D39 Source Type: research

GSE109126 Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39PcpsT= > C in medium with uracil
Contributor : Tomas G KloostermanSeries Type : Expression profiling by arrayOrganism : Streptococcus pneumoniae ; Streptococcus pneumoniae D39Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39PcpsT=>C in medium with uracil.Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae' (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Streptococcus pneumoniae Streptococcus pneumoniae D39 Source Type: research

GSE109127 Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39SM in medium with uracil
Contributor : Tomas G KloostermanSeries Type : Expression profiling by arrayOrganism : Streptococcus pneumoniae ; Streptococcus pneumoniae D39Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39SM in medium with uracil.Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae' (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Streptococcus pneumoniae Streptococcus pneumoniae D39 Source Type: research

GSE109128 Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39SM in medium without uracil
Contributor : Tomas G KloostermanSeries Type : Expression profiling by arrayOrganism : Streptococcus pneumoniae ; Streptococcus pneumoniae D39Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39SM in medium without uracil.Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae' (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Streptococcus pneumoniae Streptococcus pneumoniae D39 Source Type: research

GSE109129 Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae
Series Type : Expression profiling by arrayOrganism : Streptococcus pneumoniae ; Streptococcus pneumoniae D39This SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Streptococcus pneumoniae Streptococcus pneumoniae D39 Source Type: research

GSE109584 High-coverage TAC-seq expression
Contributors : Mariann Koel ; Kaarel Krjutskov ; Hindrek TederSeries Type : OtherOrganism : Homo sapiensTranscriptomic biomarker detection assay for targeted 57 human uters endometrium receptivity testing (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE109606 Trisomy-TAC-seq
Contributors : Hindrek Teder ; Mariann Koel ; Kaarel Krjutskov ; Tatjana JatsenkoSeries Type : OtherOrganism : Homo sapiensTAC-seq experiment to detect in vitro fetal trisomy at different range of fetal fraction. Fetal fraction ranges are 0%, 5%, 10%, 15%, 20%, 25%, 30% and 100%. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE109706 Parkinson ’s Disease Genetic Risk in a Midbrain Neuronal Cell Line
Contributors : Gerry A Coetzee ; Steven E Pierce ; Trevor TysonSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensIn genome-wide association studies of complex diseases, many risk polymorphisms are found to lie in non-coding DNA and likely confer risk through allele-dependent differences in gene regulatory elements. However, because distal regulatory elements can alter gene expression at various distances on linear DNA, the identity of relevant genes is unknown for most risk loci. In Parkinson ’s disease, at least s...
Source: GEO: Gene Expression Omnibus - March 1, 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

GSE109829 Actomyosin-mediated tension orchestrates uncoupled respiration in adipose tissues
Contributor : Timblin GregSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe activation of brown/beige adipose tissue (BAT) metabolism and the induction of uncoupling protein-1 (UCP1) expression are essential for BAT-based strategies to improve metabolic homeostasis. Adrenergic signaling is viewed as a key regulator of thermogenesis and UCP1-expression in BAT, while also operating as a potent contractile stimulator in muscle. The muscle-like gene expression patterns of UCP1+ adipocytes have previously been utilized as tissue specific markers, but have not been attributed with any fun...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE109870 transcriptome studies of BRD4 inhibitor BDF-1253 on renal clear carcinoma 786-O cells
In this study, a novel category of BRD4 inhibitors, which are originated from an approved drug Nitroxoline and its analogues, were synthesized and evaluated by biochemical and cellular assays, as well as the method of crystallography and xenograft mice models. In renal cell carcinoma cell lines, these compounds exhibited efficient inhibition against the expression and protein abundance of BRD4 downstream genes. Moreover, the complex crystal structures of several compounds in this series with the first bromodomain of BRD4 were solved, which revealed the binding mechanism of this novel category of BRD4 inhibitors and facilit...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109920 Expression data from KP and KPY murine sarcoma tumors
Contributors : T S Eisinger ; Shuai YeSeries Type : Expression profiling by arrayOrganism : Mus musculusYAP depletion in the KP tumor system results in smaller tumors and delayed tumor latency.We used microarrays to investigate changes in global gene expression due to YAP1 loss in KP tumors (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE109923 Expression data from murine sarcoma cells treated with either DMSO or a combination of SAHA and JQ1 for 48 hours
Contributors : T S Eisinger ; Adrian Rivera-ReyesSeries Type : Expression profiling by arrayOrganism : Mus musculusSAHA/JQ1 reduces in vivo tumorigenesis and proliferation of KP sarcoma cells. This model recapitulates human undifferentiated pleomporphic sarcoma (UPS).We used microarrays to investigate changes in global gene expression in response to these drugs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE110051 GRNs driving cartilage and bone formation interact via averaging and synergism during cartilage maturation
Contributors : Amir M Ashique ; Katie Ovens ; Patsy G ómez-Picos ; Ian McQuillan ; Brian EamesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTranscriptional control of any biological process occurs through the action of one to many gene regulatory networks (GRNs), but studies analyzing GRN interaction are lacking. To address this, we tested for the first time in vivo the hypothesis that two independent GRNs, which are active during formation of two discrete skeletal cell types (immature chondrocytes and osteoblasts), interact during differentiation of a third skeletal cell typ...
Source: GEO: Gene Expression Omnibus - March 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110110 targeted allele counting by sequencing (TAC-seq)
Series Type : Other ; Non-coding RNA 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 - March 1, 2018 Category: Genetics & Stem Cells Tags: Other Non-coding RNA profiling by high throughput sequencing Homo sapiens synthetic construct Source Type: research