GSE129926 The impact of hnRNP-A2B1 on mRNA transport after DNA virus infection
Contributors : Lei Wang ; Mingyue Wen ; Xuetao CaoSeries Type : Expression profiling by arrayOrganism : Mus musculusTo obtain a wholistic view of hnRNP-A2B1 ’s role in mRNA transport in response to DNA virus infection, we profiled RNAs from nuclear and cytoplasmic fractions in both wild-type and Hnrnpa2b1–/– macrophages after Herpes simplex virus 1 (HSV-1) infection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE68343 Human glioblastoma stem cells (GSCs) differentiation: Undifferentiated cells vs. Differentiated cells
Contributors : Hao Li ; Yong Cao ; Jizong ZhaoSeries Type : Non-coding RNA profiling by array ; Expression profiling by arrayOrganism : Homo sapiensUsing four patient-derived GSCs lines and their induced differentiating counterparts, we performed high-throughput microarray analysis to identify the profile changes of lncRNAs and mRNAs. The differentiation status was determined by Immunofluorescence and qRT-PCR. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Expression profiling by array Homo sapiens Source Type: research

GSE85197 RNA-seq of N2a cells treated with 100 nM Dexamethasone for 4 hours +/- siARGLU1
Contributors : Lilia Magomedova ; Serge Gueroussov ; Manuel Irimia ; Benjamin J Blencowe ; Carolyn L CumminsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusARGLU1 was identified in a screen for new modulators of glucocorticoid signaling in the CNS. RNA-seq of neuronal cells ±siARGLU1 revealed significant changes in the expression and alternative splicing of distinct genes involved in neurogenesis. Treatment with dexamethasone, a GR activator, also induced changes in the pattern of alternatively spliced genes, highlighting an underappreciated global mechanism of glucoc orticoid ...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE87358 miRNA expression in a time-series EMT process of 0h, 24h and 96h via next-generation sequencing
Contributors : Yuwei Liu ; Mengzhu XueSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to explore miRNA expressions in a time-series EMT process of 0h, 24h and 96h. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE95719 Global Gene Changes in Hearts from CardioGRMRdKO Mice
Contributors : Robert H Oakley ; John A CidlowskiSeries Type : Expression profiling by arrayOrganism : Mus musculusHeart failure is one of the leading causes of death in the Western world, and stress is increasingly associated with adverse cardiac outcomes. Glucocorticoids are primary stress hormones that regulate homeostasis through two closely related nuclear receptors, the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR). Cardiomyocytes express both receptors but little is known concerning their coordinated actions in heart physiology and pathology. To examine the in vivo function of glucocorticoid signa...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE95727 Global Gene Changes in Hearts from CardioGRKO Mice
Contributors : Robert H Oakley ; John A CidlowskiSeries Type : Expression profiling by arrayOrganism : Mus musculusHeart failure is one of the leading causes of death in the Western world, and stress is increasingly associated with adverse cardiac outcomes. Glucocorticoids are primary stress hormones that regulate homeostasis through two closely related nuclear receptors, the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR). Cardiomyocytes express both receptors but little is known concerning their coordinated actions in heart physiology and pathology. To examine the in vivo function of glucocorticoid signa...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE95732 Global Gene Changes in Hearts from CardioMRKO Mice
Contributors : Robert H Oakley ; John A CidlowskiSeries Type : Expression profiling by arrayOrganism : Mus musculusHeart failure is one of the leading causes of death in the Western world, and stress is increasingly associated with adverse cardiac outcomes. Glucocorticoids are primary stress hormones that regulate homeostasis through two closely related nuclear receptors, the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR). Cardiomyocytes express both receptors but little is known concerning their coordinated actions in heart physiology and pathology. To examine the in vivo function of glucocorticoid signa...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE95737 Global Gene Changes in Hearts from Mice with Conditional Knockout of GR, MR, or both GR and MR in Cardiomyocytes
Series Type : Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE98124 Direct Induction of the Three Pre-Implantation Blastocyst Cell Types from Fibroblasts
Contributors : Mohammad Jaber ; Hana Benchetrit ; Shulamit Baror-Sebban ; Valery Zayt ; Oren Ram ; Tommy Kaplan ; Michal Inbar ; Yossi BuganimSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusATAC-seq, RNA-seq and ChIP-seq in induced TSC and PSC 72 hours past Doxycyclin induction (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE100529 Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [SNP_genotyping]
Contributors : Toshima Z Parris ; Elisabeth W R önnerman ; Hanna Engqvist ; Jana Biermann ; Katarina Truvé ; Szilárd Nemes ; Eva Forssell-Aronsson ; Giovanni Solinas ; Anikó Kovács ; Per Karlsson ; Khalil HelouSeries Type : Genome variation profiling by SNP arrayOrganism : Homo sapiensSNP genotyping of human breast tumors (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array Homo sapiens Source Type: research

GSE100799 Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [RNA-seq]
Contributors : Toshima Z Parris ; Elisabeth W R önnerman ; Hanna Engqvist ; Jana Biermann ; Katarina Truvé ; Szilárd Nemes ; Eva Forssell-Aronsson ; Giovanni Solinas ; Anikó Kovács ; Per Karlsson ; Khalil HelouSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTranscriptomic profiling of human breast tumors using RNA sequencing (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE101411 Transcriptomic analysis of mice treated with Lactobacillus rhamnosus CNCM i-3690 and different mutants and variants generated from this strain
Contributors : Rebeca Martin ; Philippe Langella ; Tamara SmokvinaSeries Type : Expression profiling by arrayOrganism : Mus musculuswe have performed transcriptomic analysis of colonic samples of mice challenged with DNBS twice in a chronic model of inflammation and treated with CNCM -I3690 strain and several mutants and variants generated from it. colonic transcriptome analysis at the endpoint revealed that CNCM I 3690 enhances the expression of genes related to healthy gut permeability, motility (Ghrelin (GHR)), and absorption (guanylate cyclase activator 2B (Guca 2b)); cell proliferation (amino acid transporter SLC7A7);...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104089 Cell type-specific dysregulation of ERK signaling impairs synaptic plasticity and memory in a mouse model of Noonan syndrome
We report transcriptome data from excitatory and inhibitory neurons of mouse brain. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110663 H3K4me3 and H3K27me3 modification profiling in early zebrafish embryo
Contributors : Wei Zhu ; Jiang LiuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Danio rerioMulticellular organism requires concise gene regulation during ontogeny and epigenetic modifications, such as DNA methylation and histone modification, facilitate the concise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described but knowledge of how histone modifications are passed on to zygote from gametes are limited and conservations of histone modifications are not clear.We profiled H3K4me3/H3K27me3 modifications in gametes and ear...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Danio rerio Source Type: research

GSE110728 Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer ’s disease pathology and cognitive symptoms (Bisulfite-Seq)
Contributors : Peipei Li ; Lee Marshall ; Gabriel Oh ; Jennifer L Jakubowski ; Daniel Groot ; Yu He ; Ting Wang ; Arturas Petronis ; Viviane LabrieSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensEpigenetic control of enhancers alters neuron functions and may be involved in Alzheimer ’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology ( n...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE110731 Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer ’s disease pathology and cognitive symptoms (RNA-Seq)
Contributors : Peipei Li ; Lee Marshall ; Gabriel Oh ; Jennifer L Jakubowski ; Daniel Groot ; Yu He ; Ting Wang ; Arturas Petronis ; Viviane LabrieSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEpigenetic control of enhancers alters neuron functions and may be involved in Alzheimer ’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology ( n=...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE110732 Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer ’s disease pathology and cognitive symptoms
Series Type : Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Homo sapiensEpigenetic control of enhancers alters neuron functions and may be involved in Alzheimer ’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology ( n=101). We identify 1,224 differentially methylated enhancer regions; most of which are hypomet...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113424 Modulation of the ATM/autophagy pathway tips the balance between senescence and apoptosis in response to 20A ligand
Contributors : Jennifer Beauvarlet ; Paul B Sadoun ; Elodie Darbo ; Gaelle Labrunie ; Beno ît Rousseau ; Elodie Richard ; Rabindra N Das ; Guillaume Robert ; Jean-William Dupuy ; Francois Orange ; Sabrina Croce ; Valerie Valesco ; Pierre Soubeyran ; Kevin Ryan ; Jean-Louis Mergny ; Mojgan Djavaheri-MergnySeries Type : Expression profiling by arrayOrganism : Homo sapiensG-quadruplex ligands (G4L) exert their anti-proliferative effect through telomere-dependent and -independent mechanisms, but the inter-relationship between autophagy, cell growth arrest and cell death induced by these ligands remains largely unexplored...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE114904 Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments
Contributors : Adrian G Torres ; Oscar Reina ; Camille Stephan-Otto Attolini ; Llu ís Ribas de PouplanaSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensThe human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115362 The histone H3K4 demethylase JMJ16 represses leaf senescence in Arabidopsis
Contributors : Peng Liu ; Shuaibin Zhang ; Bing Zhou ; Xi Luo ; Xiao F Zhou ; Bin Cai ; Yin H Jin ; Jinxing Lin ; Xiaofeng Cao ; Jing B JinSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Arabidopsis thalianaLeaf senescence is governed by a complex regulatory network involving dynamic reprogramming of gene expression. Recent evidence indicates that trimethylation of histone H3 at lysine 4 (H3K4me3) alters gene expression during leaf senescence. However, it is largely unknown how histone modification is regulated in an age-dependent...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE117416 A comprehensive map of intron branchpoints and lariat RNAs in plants
Contributors : Binglian Zheng ; Yun ZhengSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaLariat is formed by excised intron, in which the 5' splice site joints with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by DBR1 (RNA debranching enzyme 1), recent findings in animals showed that many lariat RNAs were widely detected under physiological conditions. In contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing datasets to document plant BPs and la...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE118036 Identification of CITED2 and PU.1 target genes in human CB
Contributor : Hein SchepersSeries Type : Expression profiling by arrayOrganism : Homo sapiensCB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT3L and TPO for 12 hrs. Cells were transduced with control, CITED2 overexpression lentivectors, shRNA PU.1 lentivectors or both, in two rounds over 48 hrs. Transduced cells were sorted after which RNA was isolated for Illumina beadchip arrays HT12 v4 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE119497 XX sex chromosome complement promotes hyperlipidemia and atherosclerosis in mice
Contributors : Eric M Blalock ; Yasir AlSiraj ; Sean E Thatcher ; Ryan Temel ; Lei Cai ; Wendy Katz ; Heba M Ali ; Michael Petriello ; Andrew Morris ; Arthur P Arnold ; Karen Reue ; Patrick Tso ; Lisa CassisSeries Type : Expression profiling by arrayOrganism : Mus musculusIt is well recognized that men and women differ in circulating lipid profiles and consequently coronary artery disease (CAD). While sex hormones like estrogens are thought to protect women from CAD risk by promoting protective lipid profiles, hormone replacement therapy in women paradoxically increases CAD risk. Biological sex is determined by both sex ch...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120617 The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation
Contributors : Julia Batki ; Jakob Schnabl ; Juncheng Wang ; Dominik Handler ; Veselin I Andreev ; Christian E Stieger ; Maria Novatchkova ; Lisa Lampersberger ; Kotryna Kauneckaite ; Karl Mechtler ; Dinshaw Patel ; Julius BrenneckeSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Drosophila melanogasterThe PIWI-interacting RNA (piRNA) pathway protects animal genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Drosophila melanogaster Source Type: research

GSE120672 A functional unfolded protein response is required for normal vegetative development in Arabidopsis
Contributors : Yan Bao ; Diane C Bassham ; Stephen H HowellSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaThe Unfolded Protein Response (UPR) is activated in plants in response to ER stress and plays an important role in mitigating stress damage. We have analyzed an ire1a ire1b bzip17 triple mutant in Arabidopsis with defects in stress signaling and found that the mutant is also impaired in vegetative plant growth under conditions without externally applied stress. This raises the question as to whether the UPR functions in plant development in same manner as it does in respo...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE121271 High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq
We report the development and application of isogenic colony sequencing to profile heterogeneity among yeast colonies. We profiled transcriptomes of the opaque-white switching in C. albicans colonies and an ARO4 mutagenesis library in S. cerevisiae colonies. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Candida albicans Saccharomyces cerevisiae Source Type: research

GSE121683 ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis
Contributors : Wei Yuan ; Jinjin Tong ; Jincong Zhou ; Qianwen Sun ; Weiqiang QianSeries Type : OtherOrganism : Arabidopsis thalianaThe R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALBA1 binds to the DNA-RNA hybrid strand, AtALBA...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Other Arabidopsis thaliana Source Type: research

GSE122833 The NuRD complex suppresses transcriptional noise during lineage commitment
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 - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE123513 Oct1/Pou2f1 is selectively required for gut regeneration and regulates gut malignancy
Contributors : Karina V ázquez-Arreguín ; Dean TantinSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensAs part of a larger study focused on deletion of Oct1 (Pou2f1) in the mouse gut, we identify Oct1 target genes in HCT116 colon carcinomal cells, with H3K4me3 and input controls. Identified target genes are associated with mitotic stability, metabolism, stress response and malignancy. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE123707 Genome wide binding of Top2 (in WT and uls1 delta cells) and Uls1 (in WT cells) both in the presence and absence of the Top2 poison acriflavine (ACF)
Contributor : Helder FerreiraSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeTopoisomerase II (Top2) is an essential enzyme that decatenates DNA via a transient Top2-DNA covalent intermediate. This intermediate can be stabilised by a class of drugs termed Top2 poisons, resulting in massive DNA damage. Thus, Top2 activity is a double-edged sword that needs to be carefully controlled to maintain genome stability. We show that Uls1, an ATP-dependent chromatin remodelling (Snf2) enzyme, can alter Top2 chromatin binding and prevent Top2 poisoning in yeast. Deletio...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE123927 mRNAseq in control (WT) and Nes:Cre_Qk cKO
Contributors : Yoshika Hayakawa-Yano ; Masato YanoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe sequenced mRNA from mouse E14.5 embryonic cortex to compare gene expression level and alternative splicing events between 2 control (WT) and 2 Qk cKO.A set of tissue specific splicing factors are thought to govern alternative splicing events during neural progenitors (NPC) to neuron transition by regulating neuron specific exons. Here we proposed one such a factor, RNA-binding protein Qki5, which is specifically expressed in neural stem cells. We performed mRNAseq analysis by using mRN...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE124943 Genome-wide profiling of γH2AX in Arabidopsis
Contributors : Wei Yuan ; Jincong Zhou ; Jinjin Tong ; Qianwen Sun ; Weiqiang QianSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaThe R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALB...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE124998 A Cut/cohesin axis altersthe chromatin landscape to facilitate neuroblast death
Contributors : Kristin White ; Lei ZhouSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Drosophila melanogasterCut regulates the programmed death of neural stem cells by altering cohesin levels and promoting a more open chromatin conformation to allow cell death gene expression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE125050 Alzheimer's gene expression by cell type - SFG
Contributors : Brad Friedman ; David HansenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAD patients all had Braak stages V or VI, and were also pathologically confirmed to have amyloid plaque.The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.The ID of this project in Genentech's ExpressionPlot database is PRJ0018621 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125583 RNA Expression in fusiform gyrus of AD and Control subjects
Contributors : Melanie A Huntley ; Oded Foreman ; Brad A Friedman ; Ainhoa EtxeberriaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA was purified from frozen fusiform gyrus tissue sections of autopsy-confirmed Alzheimer's cases and neurologically normal age-matched controls.89 of the 289 subjects in this study were previously analyzed in GSE95587. For these subjects, the RNA was extracted from fusiform gyrus tissue blocks distinct to those used in GSE95587. The subjects, and the corresponding identifiers in GSE95587, are indicated in the descriptions as "repeated in GSE95587:...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE126831 A temporal proteogenomic atlas of HCV-host interactions unravels cell circuits driving viral and metabolic liver disease.
Conclusion: Our integrative analyses uncover how HCV perturbs the hepatocyte cell circuits to drive chronic liver disease and hepatocarcinogenesis. This proteogenomic atlas of HCV infection provides a model for the discovery of novel drivers for viral- and non-viral induced liver disease. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE127885 Human tumor cell lines treated with 5AZA-dC vs control untreated cells.
Contributors : D M Carraro ; H P Brentani ; E T CostaSeries Type : Expression profiling by arrayOrganism : Homo sapiensEqual amounts of test and reference cDNA Cy-labeled mRNA targets were competitively hybridized against a customized cDNA platform with 4,608 ORESTES (open reading frame expressed sequences tags) representing human genes.With this microarray experiment, we found that N-Myc downstream-regulated gene 4 (NDRG4) is silenced in tumor cells and acts as a mechanistic biomarker of metastasis in ductal invasive breast tumors. While aberrant NDRG4 silencing, by DNA hypermethylation, is significantly associated with t...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE128076 The effect of doxycycline-induced expression of host-cell-factor 2 (HCF-2) proteins on the global gene expression in HEK-293 cells
Contributors : Daria Gudkova ; Oleksandr Dergai ; Viviane Praz ; Winship HerrSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHere we study the effect of doxycycline induced expression of HCF-2 (the host-cell-factor 2) proteins - HCF-2WT and its mutant HCF-2Fn3nc* on the global gene expression in HEK-293 cells. We identified 7175 genes that were differentially expressed after day 1 in any of the HCF-2WT or HCF-2Fn3nc* samples (log2 (fold change)> 0.5 or
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE129176 Interleukin-17 receptor D constitutes an alternative receptor for interleukin-17A important in psoriasis-like skin inflammation
Contributors : Yang Su ; Xiaohong ZhaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo understand the overall function of IL-17RD and IL-17RC in IL-17A signaling, RNAseq was performed with WT, Il17rc KO, and Il17rd KO primary mouse keratinocytes following IL-17A treatment along with untreated WT control. Keratinocyte from neonatal WT, Il17rd KO, and Il17rc KO mice were cultured and stimulated with IL-17A (100 ng/mL, PeproTech) for 8h. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE129321 Daedalus and Gasz recruit Armitage to mitochondria, bringing piRNA precursors to the biogenesis machinery
Contributors : Marzia Munaf ò ; Vera Manelli ; Federica A Falconio ; Ashley Sawle ; Emma Kneuss ; Evelyn L Eastwood ; Jun W Seah ; Benjamin Czech ; Gregory J HannonSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Drosophila melanogasterThe piRNA pathway is a small RNA-based immune system that silences mobile genetic elements in animal germlines. piRNA biogenesis requires a specialised machinery that converts long single-stranded precursors into small RNAs of ~25-nucleotides in length. This process involves factors that operate in two different subcellular compartments: the nuage/Yb-body...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Drosophila melanogaster Source Type: research

Gse129851 reprogramming identifies functionally distinct stages of clonal evolution in myelodysplastic syndromes
Contributors : Jasper Hsu ; Andreea Reilly ; Brian J Hayes ; Courtnee A Clough ; Eric Q Konnick ; Beverly Torok-Storb ; Suleyman Gulsuner ; David Wu ; Pamela S Becker ; Siob án B Keel ; Janis L Abkowitz ; Sergei DoulatovSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAs part of this study, we isolated induced pluripotent stem cells (iPSCs) from a patient with TP53-mutant MDS and identified loss of chromosome 5q as a cooperating genetic event. Using RNA sequencing we found that loss of chromosome 5q dysregulates genes that maintain chromosome stability, predisposing TP53-mutant ...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE129873 Identifcation of lncRNA MACC1-AS1-associated microRNAs in breast cancer cell line MDA231 using MS2-Tagged RNA Affinity Purification and miRNA-Seq
Contributors : Y Zhou ; S Chen ; W GuSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensLncRNA MACC1-AS1 is the antisense RNA of MACC1 mRNA, which is located on the sixth intronic of MACC1 gene. MACC1-AS1 is an oncogenic lncRNA in colorectal cancer. But the function role of MACC1-AS1 in breast cancer is unknown. In the present study, We used MS2-Tagged RNA Affinity Purification and miRNA-Seq to characterize microRNAs that associated with MACC1-AS1 in breast cancer cell line MDA231. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE129882 RNA-seq transcript and gene data on zika exposed and zika na ïve samples
Contributors : Andrew Kasarskis ; Ana Fernandez-Sesma ; Mayte Suarez-FarinasSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq count data at 3 timepoints was generated for Zika-exposed and Zika-na ïve individuals in order to assess associated signatures (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE129884 ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C (4C validation)
We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks. The results of the analysis on existing mouse ES Capture Hi-C data (ArrayExpress E-MTAB-2414) were validated by two 4C-seq experiments, submitted here. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE129890 Single nucleotide variants (SNVs) associated with cutaneous melanoma (CM) risk and prognosis
Contributors : Cristiane Oliveira ; Gustavo J Louren ço ; Carmen S LemeSeries Type : SNP genotyping by SNP array ; Genome variation profiling by SNP arrayOrganism : Homo sapiensAbnormalities in pigmentation-related genes alter CM risk and prognosis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: SNP genotyping by SNP array Genome variation profiling by SNP array Homo sapiens Source Type: research

GSE129895 Phosphorylation at the S2056 1 cluster of DNA-PKcs is dispensable for lymphocyte development and class switch recombination in mice.
Contributors : Xiaobin S Wang ; Jennifer L Crowe ; Zhengping Shao ; Brian J Lee ; Shan ZhaSeries Type : OtherOrganism : Mus musculusThe classical non-homologous end-joining (cNHEJ) pathway is a major DNA double-strand break repair pathway in mammalian cells and is required for lymphocyte development and maturation. The DNA-dependent protein kinase (DNA-PK) is a cNHEJ factor that encompasses the Ku70-Ku80 (KU) heterodimer and the large catalytic subunit (DNA-PKcs). In mouse models, loss of DNA-PKcs (DNA-PKcs-/-) abrogates end-processing (e.g., hairpin-opening), but not end-ligation, while expression of the kinase-dead DNA-P...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE129901 Expression analysis of S. pimpinellifolium accession LA1589 wild type, lc, fas and lc/fas NILs, SlCLV3 RNAi and SlCLV3-complementation lines during tomato floral development.
Contributors : Yi-Hsuan Chu ; Esther van der KnaapSeries Type : Expression profiling by high throughput sequencingOrganism : Solanum pimpinellifoliumThe goal of this study is to decipher the effect of the lc and fas mutations on gene expression during floral development in tomato as well as determining the effect of strongly downregulating tomato CLV3 using the RNAi strategy. The strand-specific RNA libraries were sequenced through Illumina HiSeq2000 at Genomic Resources Core Facility at Weill Cornell Medical College for 50 bp single –end sequencing. Total raw reads for each sample ranged between 20-30 millions. (Sou...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Solanum pimpinellifolium Source Type: research

GSE129906 TCR and inflammatory signals tune human MAIT cells to exert specific tissue repair and effector functions
Contributors : Emanuele Marchi ; Tianqi LengSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe sought to describe in detail human MAIT cell activation using a transcriptomic approach to define the basic transcriptome of MAIT cells in   humans and to determine how this is modulated by activation. Fresh human peripheral blood cells were obtained from three donors, and were magnetically enriched on CD8+ cells, and flow-sorted for live CD161++TCR Va7.2+ MAIT cells. These were cultured in media for 20 hours (“unstimulated”) or i n the presence of anti-CD3/CD28 TCR beads (T...
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE129908 C6 glioblastoma microRNA regulation induced by haloperidol, risperidone and clozapine
Contributor : Mao L ChenSeries Type : Non-coding RNA profiling by arrayOrganism : Rattus norvegicusAntipsychotic drugs (APDs) have been reported to ease psychotic symptoms in the clinic. miRNAs have also been identified that can regulate the expression of genes/proteins related to possible molecular mechanisms of drug action. To reveal APD-induced miRNA modulations in glial cells, we analyzed miRNA expression in subchronically APD-treated C6 cells by using a miRNA microarray. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Rattus norvegicus Source Type: research

GSE129917 Expression data from LEF siRNA transfected Jurkat cells
Contributors : Sema S Ekmekci ; Zeliha Emrence ; Burcu Salman ; Melda Sar ıman ; Neslihan Abacı ; Cumhur Ekmekci ; Çağrı GüleçSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo identify novel target genes regulated by LEF1 transcription factor in T-ALL, we examined changes in the genome-wide gene expression profile by microarray in siRNA mediated LEF1 knockdown Jurkat cells.We used microarray to determine the differential gene expression in LEF downregulated Jurkat cells by LEF1 siRNA. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research