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GSE107118 microRNA profiling in the parasite Neospora caninum using a high-throughput approach
Contributor : Jigang YinSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Neospora caninumSmall RNA libraries from N. caninum tachyzoites were analyzed using a high-throughput RNA sequencing technology combined with systematic bioinformatics analysis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Neospora caninum Source Type: research

GSE86780 Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism
Contributors : Kairui Mao ; Andrew J Martins ; Ronald N GermainSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn support of our manuscript investigating the roles of ILCs and T cells the in maintenance of gut hoemostasis, we have performed RNAseq on terminal illeum of mice lacking either all adaptive immune cells (RAG1 -/-), deficient in T cells (TCRalpha -/-), or deficient in T cells but co-housed with wild-type mice and RAG1 -/- mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE87795 Single-cell transcriptome analysis of mouse fetal livers from different developmental stages
Contributors : Xianbin Su ; Yi Shi ; Ze-Guang HanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development. Our data demonstrated the existence of two types of stem/progenitor cells with distinct molecular patterns during liver development. Both types of cells exhibit heterogeneity of transcriptional program within each cell population, suggesting they be in distinct status of self-renewa...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE89842 Diabetes Impairs Wound-Healing by let-7d-3p-dependent DNMT1 Upregulation in Hematopoietic Stem Cells
Contributors : J Yan ; G Tie ; S Wang ; L Khair ; L M MessinaSeries Type : Non-coding RNA profiling by arrayOrganism : Mus musculus ; synthetic constructTo identify microRNAs which differentially expressed in hematopoietic stem cells from wt mice and db/db miceWe used microRNA microarrays to identify miroRNAs which can directly regulate dnmt1 expression in hematopoietic stem cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Mus musculus synthetic construct Source Type: research

GSE90127 Gene array analysis of primary mouse calvaria osteoblasts without differentiation, with differentiation, or with differentiation plus cabozantinib (XL184)
Contributors : Sue-Hwa Lin ; Li-Yuan Yu-LeeSeries Type : Expression profiling by arrayOrganism : Mus musculusWe performed a gene array analysis using RNAs prepared from undifferentiated, differentiated, or differentiated + cabozantinib (XL184) treated osteoblasts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE90775 PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance
Contributors : Nilotpal Roy ; Kenneth K Takeuchi ; Jeanine M Ruggeri ; Peter Bailey ; David Chang ; Joey Li ; Laura Leonhardt ; Sapna Puri ; Megan T Hoffman ; Shan Gao ; Christopher J Halbrook ; Yan Song ; Mats Ljungman ; Shivani Malik ; Christopher Wright ; David W Dawson ; Andrew V Biankin ; Matthias Hebrok ; Howard C CrawfordSeries Type : OtherOrganism : Mus musculusAberrant activation of embryonic signaling pathways is frequent in pancreatic ductal adenocarcinoma (PDA) making developmental regulators therapeutically attractive. Here, we demonstrate diverse functions for PDX1, a transcription factor indispensable for pa...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE90822 Correlating anatomy and function with gene expression in individual neurons by combining in vivo labeling, patch clamp and single cell RNA-seq
Contributors : Carsten K Pfeffer ; Massimo ScanzianiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe classification of neurons into distinct types is an ongoing effort aimed at revealing and understanding the diversity of the components of the nervous system. Recently available methods allow us to determine the gene expression pattern of individual neurons in the mammalian cerebral cortex to generate powerful categorization schemes. For a thorough understanding of neuronal diversity such genetic categorization schemes need to be combined with traditional classification parameters l...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE96630 Single-cell transcriptome analysis of EpCAM+ cells from P3.25 mouse fetal livers
Contributors : Xianbin Su ; Yi Shi ; Ze-Guang HanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 52 EpCAM+ cells from postnatal day 3.25 mouse fetal livers. These cells show characters of cholangiocytes. Combined with our previous single cell data of E11.5~P2.5 mouse fetal livers, our data depict the dynamic trajectories with transcriptional profiles at single-cell resolution during mouse liver development, and provide insights into the fate decision and transcriptional control of sel...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE98013 Small RNAs from 11 Drosophila species
Contributors : Jaaved Mohammed ; Alex S Flynt ; Eric C LaiSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Drosophila ananassae ; Drosophila erecta ; Drosophila grimshawi ; Drosophila mojavensis ; Drosophila persimilis ; Drosophila pseudoobscura ; Drosophila sechellia ; Drosophila simulans ; Drosophila virilis ; Drosophila willistoni ; Drosophila yakubaAnnotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Drosophila ananassae Drosophila erecta Drosophila grimshawi Drosophila mojavensis Drosophila persimilis Drosophila pseudoobscura Drosophila sechellia Drosophila simulans Drosophila v Source Type: research

GSE98352 Gene expression analysis using RNA Sequencing of the Saccharomyces cerevisiae BY4741 Spt4-T42A/S43A mutant strain upon osmotic stress.
Contributors : Francesc Posas ; Eul àlia deNadalSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeTo study the relevance of the phosphorylation of Spt4 in residues T42 and S43, we assessed the genome-wide transcriptional response of the non-phosphorylatable Spt4-T42A/S43A mutant (Spt4-AA) upon osmotic stress. Results point out that the unphosphorylatable Spt4-T42A/S43A protein showed an impaired stress responsive gene expression indicating that these specific residues play a relevant role in osmotic stress responsive transcriptional regulation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE99257 Robust detection of chromosomal contacts from small cell numbers using low-input Capture-C
We present two new low-input Capture-C protocols that generate high-quality, reproducible interaction profiles from fewer than 20,000 cells, and show that these are not biased by PCR amplification or the degree of formaldehyde fixation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE106120 The histone demethylase Kdm6 regulates a mature gene expression program in differentiating cerebellar granule neurons
Contributors : Fang Liu ; Ranjula Wijayatunge ; Karl B Shpargel ; Nicole J Wayne ; Urann Chan ; Jane-Valeriane Boua ; Terry Magnuson ; Anne E WestSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe histone H3 lysine 27 (H3K27) demethylase Kdm6b (Jmjd3) can promote cellular differentiation, however its physiological functions in neurons remain to be fully determined. We studied the expression and function of Kdm6b in differentiating granule neurons of the developing postnatal mouse cerebellum. At postnatal day 7, Kdm6b is expressed throughout the layers of the developing cerebellar cor...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE106672 Long-lived mutants daf-2(e1370) and eat-2 (ad465) expression profilings
In this study, we aimed to identif y key pathways and metabolite fingerprints of longevity shared between the two interventions in worms using a multi-omics integration approach. We collected transcriptomics and metabolomics data from two long-lived mutant worm strains, i.e. daf-2 (impaired IIS pathway) and eat-2 (CR model) and compa red with N2 strain. We detected many key pathways that were upregulated at the gene expression level in both long-lived mutants, such as defense response and lipid storage, while synthesis of macromolecules and developmental processes were downregulated at the transcript level. From our polar ...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Caenorhabditis elegans Source Type: research

GSE106681 GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 1)
Contributors : Jeff S Jasper ; Kimberly J Cocce ; Logan Everett ; Suzanne Wardell ; Thomas Westerling ; Taylor Krebs ; Robert Baldi ; Tricia M Wright ; Alex Yllanes ; Jeremy T Blitzer ; Craig Logsdon ; Daniel Rakiec ; David Ruddy ; Terry Hyslop ; Allison Hall ; Jeffrey R Marks ; Gregory E Crawford ; Myles Brown ; Donald P McdonnellSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degrader...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106694 GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 2)
Contributors : Jeff S Jasper ; Kimberly J Cocce ; Logan Everett ; Suzanne Wardell ; Thomas Westerling ; Taylor Krebs ; Robert Baldi ; Tricia M Wright ; Alex Yllanes ; Jeremy T Blitzer ; Craig Logsdon ; Daniel Rakiec ; David Ruddy ; Terry Hyslop ; Allison Hall ; Jeffrey R Marks ; Gregory E Crawford ; Myles Brown ; Donald P McdonnellSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degrader...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106695 GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the developmen...
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106784 Whole genome gene microarray for diffuse gliomas
Contributors : Chang Shu ; Qiong Wang ; Jinhuan WangSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe used whole genome microarray expression profiling as a discovery platform to identify high grade diffuse glioma associated differently expressed genes comparing with low grade diffuse glioma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE75677 Comparison of Liver Tumor Models to Regenerating Liver Tissues
Contributors : Weiping Han ; Russell E EricksenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculus ; Rattus norvegicusTo identify genes and pathways sepcific to tumorigenesis, we harvested tissues from two different liver tumor models as well as regenerating tissues. Genes significantly different in the two tumor models, but not in regenerating tissues, were used for further investigation (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 19, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Rattus norvegicus Source Type: research

GSE107082 DNA methylation signatures of injection illicit drug use (IDU) and hepatitis C (HCV) predict HIV pathophysiologic frailty
Series Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE87585 The Aneuploid Multiple Myeloma 3D Genome Reveals Spatial Genome Disorganization Associated with Copy Number Variations and Gene Expression
Contributors : Tingting Li ; Lumeng Jia ; Ruifeng Li ; Pengze WuSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Genome variation profiling by high throughput sequencingOrganism : Homo sapiensHi-C technique has been widely applied to study the three-dimensional architecture of the whole genome. Genome structures such as compartment A/B, TAD (topologically associated domain) and chromatin loops can be identified from Hi-C data in both normal cells of human and other species, and are found to be associated with features such as epigenetic ma...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Genome variation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE89571 A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data
Discussion. Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE90003 Mapping nucleolus-associated chromatin interactions by nucleolus-Hi-C reveals repression network
Contributors : Tingting Li ; Haowei Meng ; Cheng LiSeries Type : OtherOrganism : Homo sapiensNucleolus plays a key role in organizing global nuclear structure and facilitating gene regulation, but the three dimensional information within the nucleolus associated chromatins are still unknown, so here we development the Nucleolus Hi-C (NHi-C) experimental technique, which combines the nucleolus isolation with Hi-C experiment, and study the interactions within and surrounding nucleolus in human cells with a high resolution. With NHi-C experiment, we report how the nucleolus-associated chromatin regions interact at genome scal...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE99101 Enhancer-binding of Brd4 controls cell differentiation
Contributors : Ji-Eun Lee ; Young-Kwon Park ; Sarah Park ; Younghoon Jang ; Nicholas Waring ; Binbin Lai ; Weiqun Peng ; Kai GeSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe epigenomic reader Brd4 is an important drug target for cancers. However, its role in cell differentiation and animal development remains largely unclear. Using two conditional knockout mouse strains and derived cells, we demonstrate that Brd4 controls cell identity gene induction and is essential for adipogenesis and myogenesis. Brd4 co-locali...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE100264 DNA methylation signatures of injection illicit drug use (IDU) and hepatitis C (HCV) predict HIV pathophysiologic frailty I
Contributors : Ke Xu ; Xinyu Zhang ; Amy JusticeSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensGenome wide DNA methylation profiling of IDU+/HCV+ and IDV-/HCV- individuals for DNA samples extracted from peripheral blood. The Illumina Infinium Human DNA methylation 450 Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 216 IDU+/HCV+ and 170 IDU-/HCV- individuals. The goal was to identify genome-wide differentially methylated CpG sites between IDU+/HCV+ and IDU-/HCV- samples. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE103307 Role of FGFR1 in neuronal devlopment
Contributor : Michal K StachowiakSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: The goal was to study the effects of nFGFR1 on neuronal progenitor cells, by analyzing different effects of FGFR1 mutants through RNA-seq. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE105420 DNA methylation profile in chronic myelomonocytic leukemia associates with distinct clinical, biological and genetic features
In this study we performed DNA methylation microarrays in 65 CMML patients and 10 healthy controls. Differential methylation analysis between patients and controls allowed us to identify abnormalities in DNA methylation including hypermethylated genes, large genome regions with aberrant DNA methylation and altered cellular pathways. Hierarchical cluster analysis identified two main clusters that associated with the clinical, biological and genetic features of patients. Group 1 was enriched in patients that presented with adverse clinical and biological characteristics and that had a poorer overall survival and progression ...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE106977 Triple negative breast cancer subtypes and pathologic complete response rate to neoadjuvant chemotherapy
Contributors : Angela Santonja ; Alfonso S ánchez-Muñoz ; Ana Lluch ; M R Chica-Parrado ; Joan Albanell ; José I Chacón ; Lourdes Calvo ; José M Jerez ; Juan de la Haba ; Vanessa de Luque ; Cristina E Fernández-De Sousa ; Luis Vicioso ; Yéssica Plata ; César L Ramírez-Tortosa ; Martina Álvarez ; Casilda Llácer ; Irene Za rcos ; Eva Carrasco ; Rosalía Caballero ; Miguel Martín ; Emilio AlbaSeries Type : Expression profiling by arrayOrganism : Homo sapiensTriple negative breast cancer is a heterogeneous disease with distinct molecular ...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE106983 Metabolic regulation of filamentous fungi is tailored for secondary secondary metabolite production
Contributors : Jens C Nielsen ; Jens NielsenSeries Type : Expression profiling by high throughput sequencingOrganism : Penicillium coprophilum ; Penicillium decumbens ; Penicillium flavigenum ; Penicillium nalgiovense ; Penicillium polonicum ; Penicillium steckiiWe investigated the metabolism of six secondary metabolite producing fungi of the Penicillium genus, during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. Coexpression analysis revealed that expression of secondary metabolite biosynthetic genes ...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Penicillium coprophilum Penicillium decumbens Penicillium flavigenum Penicillium nalgiovense Penicillium polonicum Penicillium steckii Source Type: research

GSE106984 SOX10 Single Transcription Factor Based Fast and Efficient Generation of Oligodendrocytes from Human Pluripotent Stem Cells
We report the use of a single transcription factor, SOX10, for the generation of oligodendrocytes from human pluripotent stem cells. We further used RNA sequencing to compare the oligodendrocytes derived from pluripotent stem cells to different primary cells. It was revealed that oligodendrocytes derived from pluripotent stem cells are representative of intermediate oligodendrocytes during embryonic development. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106988 Expression data from Huh7.5.1 cells transfected with siNDRG1 or siNT
Contributors : Cameron J Schweitzer ; Fang Zhang ; Audrey Boyer ; Kristin Valdez ; Maggie Cam ; T LiangSeries Type : Expression profiling by arrayOrganism : Homo sapiensHost cells harbor various intrinsic mechanisms to restrict viral infections as a first line of antiviral defense. Viruses have evolved various countermeasures against these antiviral mechanisms. Here we show that N-Myc Downstream-Reguated Gene 1 (NDRG1) limits productive HCV infection by inhibiting viral assembly. Interestingly, HCV infection down-regulates NDRG1 protein and mRNA expression. Loss of NDRG1 increases the size and number of lipid droplets, whi...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE107008 Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines IV
Contributors : Naohiko Seki ; Yasutaka YamadaSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (pancreatic cancer, esophageal cancer and lung squamous cell carcinoma) were subjected to Agilent whole genome microarrays. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE107015 Gene expression data from whole blood of a Phase II randomized clinical trial of the treatment of methamphetamine dependence with topiramate
Contributors : Ming D Li ; Ju Wang ; Tianhua Niu ; Jennie Z Ma ; Chamindi Seneviratne ; Nassima Ait-Daoud ; Jim Saadvandi ; Rana Morris ; David Weiss ; Jan Campbell ; William Haning ; David J Mawhinney ; Denis Weis ; Michael McCann ; Christopher Stock ; Roberta Kahn ; Erin Iturriaga ; Elmer Yu ; Ahmed ElkashefSeries Type : Expression profiling by arrayOrganism : Homo sapiensA genome-wide RNA expression study based on a Phase II randomized placebo-controlled clinical trial of topiramate (TPM) treatment of methamphetamine (METH) dependence.Gene expression data were analyzed based on TPM responses at Weeks 8 and 12, to identi...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE107040 Alteration in gene expression levels in glioblastoma cells in response to fractionated irradiation
Contributors : Ki-Chun Yoo ; Yongjoon SuhSeries Type : Expression profiling by arrayOrganism : Homo sapiensAnalysis of alteration in gene expression levels in response to irradiation. The aim of this study was to screen genes associated with radioresistance and infiltration of glioblastoma (GBM) cells after radiotherapy. Results provide importance information of the response of GBM cells to ionizing radiation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE107080 DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty II
Contributors : Ke Xu ; Xinyu Zhang ; Amy JusticeSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensThis dataset is used as replication set for Illumina 450k. Genome wide DNA methylation profiling of IDU+/HCV+ and IDV-/HCV- individuals for DNA samples extracted from peripheral blood. The Illumina Infinium Human DNA methylation 450 Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 216 IDU+/HCV+ and 170 IDU-/HCV- individuals. The goal was to identify genome-wide differentially methylated CpG sites between IDU+/HCV+ and IDU-/HCV- samples. (Sou...
Source: GEO: Gene Expression Omnibus - November 17, 2017 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE106963 Rhinovirus infection of polarized human macrophages induces differential gene expression
Contributors : Charu Rajput ; Megan P Walsh ; Breanna N Eder ; Ediri E Metitiri ; Antonia P Popova ; Marc B HershensonSeries Type : Expression profiling by arrayOrganism : Homo sapiensExpression profiling of differentially polarized human macrophages in response to Rhniovirus A16 treatment (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE94488 Harnessing BET inhibitor sensitivity reveals AMIGO2 as a melanoma survival gene.
Contributors : Barbara Fontanals-Cirera ; Dan Hasson ; Chiara Vardabasso ; Eva Hernando ; Emily BernsteinSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe utilize the transcriptional effects of BETi in melanoma and identify AMIGO2 as a direct target gene essential for melanoma cell survival both in vitro and in vivo. We further map the enhancer landscape of NHM and melanooma and show that genes regulated by super enhancers are expressed in higher levels, exihibit higher sensitivity to BETi, and over expressed in melan...
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104657 Polycomb Repressive Complex 2 methylates Elongin A to regulate transcripiton [RNA-seq]
Contributors : M B Ardehali ; Anthony AnselmoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPolycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required to maintain gene repression during development. Misregulation of PRC2 is linked to a range of neoplastic malignancies, which is believed to involve methylation of H3K27. However, the full spectrum of non-histone substrates of PRC2 that might also contribute to PRC2 function is not known. We characterized the target recognition specificity of PRC2 and used the resultant data to screen for novel ...
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE104658 Polycomb Repressive Complex 2 methylates Elongin A to regulate transcripiton [BrU-RNA-seq]
Contributors : M B Ardehali ; Anthony AnselmoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPolycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required to maintain gene repression during development. Misregulation of PRC2 is linked to a range of neoplastic malignancies, which is believed to involve methylation of H3K27. However, the full spectrum of non-histone substrates of PRC2 that might also contribute to PRC2 function is not known. We characterized the target recognition specificity of PRC2 and used the resultant data to screen for novel ...
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE104659 Polycomb Repressive Complex 2 methylates Elongin A to tune transcript levels of targeted genes [ChIP-seq]
Contributors : M B Ardehali ; Anthony AnselmoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusPolycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27). PRC2 is required to maintain gene repression during development and differentiation and misregulation of PRC2 is linked to a range of neoplastic malignancies, activities that are believed to involve H3K27 methylation. The full spectrum of non-histone substrates of PRC2, however, is not known, and it is not known which other substrates might also contribute to the biological functions of PRC2. We...
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE104660 Polycomb Repressive Complex 2 methylates Elongin A to regulate transcription
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 - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE106902 DNA methylation profiling of genomic DNA isolated from urine in Diabetic Chronic-Kidney Disease: a pilot study
Contributor : Alexandra Sexton-OatesSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensGenome wide DNA methylation profiling of urine and blood samples from patients with diabetic chronic kidney disease. The Illumina Infinium MethylationEPIC BeadChip kit was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Samples included two urine and four buffy coat samples from adults with diabetic chronic kidney disease. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE106916 Myc regulates gene expression in P493-6 cell lines which carry a Myc tet-off system
Contributors : Mian Wu ; Pengfei Zhang ; Limian CaoSeries Type : Expression profiling by arrayOrganism : Homo sapiensIn order to study the Myc-regulated gene, we have employed whole genome mRNA/ncRNA microarray expression profiling as a discovery platform to identify genes with the potential to be regulated by Myc. Furthermore, we studied whether some Myc-regulated ncRNAs mediated the function of Myc. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE106917 The impact of lncRNA LAST knockdown on gene expression profile in HCT116 cells
Contributors : Mian Wu ; Limian Cao ; Pengfei ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHigh-throughput sequencing was employed to analyze the genes whose expression are altered when lncRNA LAST is downregulated by shRNA in HCT116 cells. The Gencode Gene ID of lncRNA LAST is ENSG00000254682.1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106918 Identification of CNBP binding mRNA and the binding sites/motifs in HCT116 cells
Contributors : Mian Wu ; Limian Cao ; Pengfei ZhangSeries Type : OtherOrganism : Homo sapiensHigh-throughput RNA-IP sequencing was employed to identify the CNBP binding mRNAs and their binding sites in HCT116 cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE106954 Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsAFB6 overexpression mutant Transcriptomes
Contributors : Qin He ; Yongzhong XingSeries Type : Expression profiling by high throughput sequencingOrganism : Oryza sativaPurpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transgene-derived OsAFB6 overexpression mutant transcriptome profiling (RNA-seq) to microarrayMethods: young panicle( (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Source Type: research

GSE106959 Time-course hypoxia incubation (1% O2) of D283-Med medulloblastoma cells
Contributors : Yuen N Fan ; Violaine SeeSeries Type : Expression profiling by arrayOrganism : Homo sapiensElucidation of the impact of hypoxia in D283-Med (medulloblastoma Homo sapiens, human, ATCC ® HTB-185™) cells to depict molecular mechanisms, which could explain drug resistance when cells are exposed to long-term hypoxia (5 days).Global gene expression study by microarray analysis to allow an efficient search for a range of genes. D283-MED cells were incubated for a varied hypoxic duration (0, 6, 64 and 96 hours in triplicate), cDNA samples were prepared and sent directly to NimbleGen. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 16, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE106847 The Unfolded Protein Response Regulator, ATF6, Promotes Mesodermal Differentiation
Contributors : Heike Kroeger ; Evan T Powers ; R L Wiseman ; Jonathan H LinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensATF6 encodes a transcription factor that is activated during the Unfolded Protein Response to protect cells from ER stress. Loss of ATF6 α and its paralog ATF6β, results in embryonic lethality, notochord dysgenesis, and in people, loss of ATF6α specifically, results in malformed neuroretina and congenital vision loss. These phenotypes implicate an essential role for ATF6 during vertebrate development. We investigated the function of ATF6 in develo...
Source: GEO: Gene Expression Omnibus - November 15, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE70746 aCGH from mouse gPAK testicular teratocarcinomas
Contributors : Amy M Lyndaker ; Claire Anderson ; Robert S WeissSeries Type : Genome variation profiling by genome tiling arrayOrganism : Mus musculusTesticular germ cell tumors are among the most responsive solid cancers to conventional chemotherapy. To elucidate the underlying mechanisms, we developed a mouse testicular germ cell tumor model in which germ cell-specific oncogenic Kras activation and tumor suppressor Pten inactivation was driven by CRE-mediated recombination. The resulting mice rapidly developed malignant, metastatic testicular cancers composed of both teratoma and embryonal carcinoma, the latter of which ...
Source: GEO: Gene Expression Omnibus - November 14, 2017 Category: Genetics & Stem Cells Tags: Genome variation profiling by genome tiling array Mus musculus Source Type: research

GSE88856 JNK promotes epithelial cells anoikis by transcriptional and post-translational regulation of BH3-only proteins
Contributors : Nomeda Girnius ; Roger J DavisSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDevelopmental morphogenesis, tissue injury, and oncogenic transformation can cause the detachment of epithelial cells. These cells are eliminated by a specialized form of apoptosis (anoikis). While the processes that contribute to this form of cell death have been studied, the underlying mechanisms remain unclear. Here we tested the role of the cJUN NH2-terminal kinase (JNK) signaling pathway using murine models with compound JNK-deficiency in mammary and kidney epithelial cells. These studies...
Source: GEO: Gene Expression Omnibus - November 14, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE89855 Gene expression in green millet (Setaria viridis): developmentally regulated genes, transcription start sites, and stimulating introns
Contributors : Alan B Rose ; Ian W Davis ; Jennifer P To ; Matthew S Marengo ; Tedd D ElichSeries Type : Expression profiling by high throughput sequencingOrganism : Setaria viridisSetaria viridis (green millet) is gaining popularity as a model C4 monocot due to its small size, rapid life cycle, and compact, sequenced genome. To analyze the structure and regulation of genes throughout development, the transcriptomes of 13 tissues at different stages of development were determined by RNA sequencing, and transcription start sites were mapped. Genes were identified that are differentially expressed in different developmental ...
Source: GEO: Gene Expression Omnibus - November 14, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Setaria viridis Source Type: research