GSE112389 Vitis Myb14 confer cold and drought tolerance by mediated nsLTP genes expression and ABA signaling passway in arabidopsis
Contributors : Linchuan Fang ; Nian Wang ; Xiaoming Sun ; Lingye Su ; Shaohua Li ; Haiping XinSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaThe growth and fruit quality of grapevine are widely affected by abnormal climatic conditions such as extreme temperature. But how grapevine responds to cold stress is still largely unknown. Here we found that VaMyb14, a member of R2R3 Myb transcription factor family, was up-regulated dramatically during cold, drought and salinity treatments in Vitis amurensis, a cold and drought-hardiness wild Vitis species. Overexpression VaMyb14 in Arabidopsis increased a...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE112787 Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs
Contributors : Paul Vogel ; Matin Moschref ; Qin Li ; Tobias Merkle ; Karthika D Selvasaravanan ; Jin B Li ; Thorsten StafforstSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMolecular tools to target RNA site ‐specifically allow recoding of RNA information and processing. SNAP‐tagged deaminases, guided by a chemically stabilized guideRNA, enable the simultaneous editing of targeted adenosine to inosine in several endogenous transcripts, with high efficiency (up to 90%), high potency, sufficient durat ion, and high precision. We applied SNAP‐ADARs for the efficient and concurren...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113034 Gene expression profiling of tumor-associated macrophages and in-vitro cultured macrophages
Contributors : J N Arnold ; J CaronSeries Type : Expression profiling by arrayOrganism : Mus musculusThe aim of this study was to decipher gene expression of tumor-associated macrophage in the 4T1 mouse model of breast cancer. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE113248 A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription in Trans
Contributors : Pei-Fang Tsai ; Stefania Dell ’Orso ; Joseph Rodriguez ; Karinna O Vivanco ; Kyung-Dae Ko ; Kan Jiang ; Aster H Juan ; Aishe A Sarshad ; Laura Vian ; Michelle Tran ; Dara Wang ; A H Wang ; Jelena Perovanovic ; Dimitros Anastasakis ; Evelyn Ralston ; Thomas Ried ; Hong-Wei Sun ; Markus Hafner ; Daniel R Larson ; Vit torio SartorelliSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe enhancer regions of the myogenic master regulator MyoD give rise to at least two enhancer RNAs. CEeRNA regulates transcription of the adjacent MyoD gene while DRReRNA affe...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE113693 Connexin 30 deficiency attenuates A2 astrocyte responses and induces severe neurodegeneration in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride Parkinson ’s disease animal model
Contributors : Atsushi Fujita ; Hiroo Yamaguchi ; Ryo Yamasaki ; Tiwen Cui ; Yuta Matsuoka ; Ken-ichi Yamada ; Jun-ichi KiraSeries Type : Expression profiling by arrayOrganism : Mus musculusCx30 deficiency induced acceleration of dopaminergic neuron death upon MPTP toxicity. Gene expressions in the striatum of wild type and Cx30 KO mice after MPTP treatment were different in the aspect of neuroprotective A2 response. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE113725 DNA methylation and inflammation marker profiles associated with a history of depression.
In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n=100) and individuals without a history of depression (n=100) using the Illumina 450K microarray. Our analysis identified 6 significant (Sidak corrected  P
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE113839 RNA-seq from HNSCC and melanoma populations
Contributor : Andrew GentlesSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPopulations were sorted from tumor speciments via flow cytometry using EPCAM, FAP, CD45, and CD31 surface markers (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113885 Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [E6.5 to E9.5]
Contributors : L Beccari ; N MorisSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGastruloids are small aggregates of murine Embryonic Stem (ES) cells stimulated to undergo gastrulation-like symmetry breaking events in vitro (van den Brink, S. C. et al. 2014, Simunovic, M.& Brivanlou, A. H 2017). We analyzed the transcriptomic profiles of gastruloids at different time-points after aggregation (AA) and compared them with those of mouse embryo at different stages, raging from e6 to e9.5. We show that gastruloids are capable of organizing a post-occipital pattern of neural, mesoderma...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114105 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 (PRKAA1) knockdown effect on the transcriptome of primary human acute myeloid leukemia (AML) cells
Contributors : Mohammad Minhajuddin ; Craig T JordanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo explore the function of AMPK signaling in acute myeloid leukemia (AML), we used shRNA to knock down the expression of PRKAA1, the catalytic subunit of the 5'-prime-AMP-activated protein kinase (AMPK), in primary human AML cells and performed RNA-seq experiment to profile transcriptional changes upon AMPK inactivation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114106 Mitochondrial Fission 1 (FIS1) knockdown effect on the H3K27Ac status of leukemia cell line MOLM-13 cells
Contributors : Shanshan Pei ; Craig T Jordan ; Stephen C Mack ; Sisi Lai ; Jeremy N RichSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo examine if loss of FIS1 would alter the H3K27Ac status of leukemic cells, we used shRNA to knock down the expression of FIS1 in leukemic cell line MOLM-13 cells and performed H3K27Ac CHIP-seq to characterize any changes in the H3K27Ac marks upon loss of FIS1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114109 Mitochondrial Fission 1 (FIS1) knockdown effect on the transcriptome of primary human acute myeloid leukemia (AML) cells
Contributors : Shanshan Pei ; Craig T JordanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo explore the function of Mitochondrial Fission 1 (FIS1) in acute myeloid leukemia (AML), we used shRNA to knock down the expression of FIS1 in primary human AML cells and performed RNA-seq experiments to profile global gene expression changes upon FIS1 depletion. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114111 Mitochondrial Fission 1 (FIS1) knockdown effect on the transcriptome of leukemia cell line MOLM-13 cells
Contributors : Shanshan Pei ; Craig T JordanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo explore the function of Mitochondrial Fission 1 (FIS1) in acute myeloid leukemia (AML), we used shRNA to knock down the expression of FIS1 in leukemia cell line MOLM-13 cells and performed RNA-seq experiments to profile transcriptional changes upon FIS1 depletion. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114126 Comparing the Transcriptomes of Wild Type (WT) and Gdf9-Cre or Zp3-Cre mediated Mtor Oocyte-Conditional Knockout (referred to as MG and MZ, respectively) Mouse GV-stage fully-grown oocytes (FGO) by RNA-Seq Analysis
Contributor : You-Qiang SuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study is to identify the differentially expressed genes in Gdf9-Cre and Zp3-Cre mediated Mtor oocyte-specific knockout (CKO) GV-stage fully-grown oocytes (FGO) by comparing their transcriptomes with that of the wild-type (WT) via RNA-Seq Analysis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114298 Targeting EZH2 reprograms intratumoral regulatory T cells to enhance cancer immunity
This study reveals a novel strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114471 In-Vivo Expansion of Cancer Stemness Affords Novel Cancer Stem Cell Targets: Malignant Rhabdoid Tumor as an Example
Contributors : Tomer Kalisky ; Itamar KanterSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer stem cell (CSC) identification relies on transplantation assays of cell sub-populations sorted from fresh tumor samples. Herein, we attempt to bypass limitations of abundant tumor source and predetermined immune selection by in-vivo propagating patient derived xenografts (PDX) from human malignant rhabdoid tumor (MRT), a rare and lethal pediatric neoplasm, to an advanced state in which most cells behave as CSCs. Stemness is then probed by comparative transcriptomics of serial PDXs genera...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114579 Trim27 confers myeloid hematopoiesis competitiveness by upregulating myeloid master genes
Contributors : Tongjie Wang ; Yong Dong ; Jinyong WangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNAseq were performed to analyze the transcriptomic differences between Trim27-overexpressing MP and empty vector control MP (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114630 Profiling of murine resident adipose tissue and aortic macrophages according to their expression status of LYVE-1
Contributors : Lim H Ying ; Daniel Carbajo ; Josephine LumSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBeside their role in conventional immune regulation, macrophages are now recognised as essential regulator of local tissue homeostasis depending on the tissue in which they reside. Using phenotyping, we found that LYVE-1+ macrophages are the major resident macrophage population in murine aorta and adipose tissues under steady state. Furthermore, imaging analysis revealed the exclusive association of adipose tissue LYVE-1+ macrophages with smooth muscle positive large blood vessels...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114850 RNA expression following TMPRSS11B overexpression or depletion
Contributors : Barrett L Updegraff ; Xiaorong Zhou ; Yabin Guo ; Pei-Hsuan Chen ; Chendong Yang ; Jessica Sudderth ; Carla Rodriguez-Tirado ; Luc Girard ; John D Minna ; Prashant Mishra ; Ralph J Deberardinis ; Kathryn A O'DonnellSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: We are analyzing differential gene expression in human bronchial epithelial cells with TMPRSS11B overexpression or control GFP, as well has human lung squamous cell cancer line HCC2814 with inducible knockdown of TMPRSS11B or control. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114916 RNA transcriptome analysis of IRF1 and IRF3 knockout in immortalized primary hepatocytes infected with hepatitis A virus
Contributors : Daisuke Yamane ; Sara R Selitsky ; Praveen Sethupathy ; Stanley M LemonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensInterferon regulatory factors (IRFs) play key roles in the transactivation of antiviral genes at the step downstream of activated pathogen-associated molecular pattern sensors, such as RIG-I-like receptors or Toll-like receptors. Whereas IRF1 and IRF3 are thought to bind similar DNA elements (ISRE and PRD-III, PRD-I) to activate antiviral gene transcription, genome-wide transcriptome profiling of IRF1 versus IRF3 knockouts in an immortalized primary hep...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114959 Oncogenic properties of NEAT1 in prostate cancer cells depend on the CDC5L-AGRN transcriptional regulation circuit
Contributors : Xin Li ; Zhengtao Xiao ; Rongyao Huang ; Xuerui YangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSilencing NEAT1 in prostate cancer cells repressed the transcriptional activity of CDC5L, and RNA-seq and further analyses revealed a handful of potential targets of CDC5L regulated by NEAT1 expression. We have established the requirement of the CDC5L-AGRN circuit for the essential oncogenic role of NEAT1 in prostate cancer cells. Here we provide processed raw counts files. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115131 Overexpression of chicken IRF7 increased viral replication and programmed cell death to the avian influenza virus infection through TGF-beta/FoxO signaling axis in DF-1
Contributors : Tae-Hyun Kim ; Huaijun ZhouSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallusTo elucidate the functional role of chicken IRF7 against avian influenza virus (AIV) infection, we generated inducible IRF7 overexpression DF-1 cell lines that could fine control the IRF7 expression level and performed in vitro infection using low pathogenic AIVs (LPAIVs) followed by RNA-seq. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Gallus gallus Source Type: research

GSE115138 Enhanced susceptibility of cancer cells to oncolytic rhabdo-virotherapy by expression of Nodamura virus protein B2 as a suppressor of RNA interference
Contributors : Donal Bastin ; Adrian Pelin ; Carolina S IlkowSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe have evaluated the response of M14 cells to VSV virus expressing eGFP or insect virus B2 protein.We find interferon related genes to be at higher levels when cells are infected with VSV-B2 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE115144 Transcriptome analysis of paired luminal breast tumor and para-carcinoma tissues
Contributors : Wei Sun ; Xiaoen Xu ; Yizhou Jiang ; Xi Jin ; Ping Zhou ; Yirong Liu ; Zhiming ShaoSeries Type : Expression profiling by arrayOrganism : Homo sapiensWith stringent filtering criteria (fold change>2, p (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE115165 Whole transcriptome profiling by RNA-sequencing of RNA from N2 and F01D4.5(baf20) C. elegans
Contributors : Alfred L Fisher ; Brett R IpsonSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansA forward genetic screen identified a mutation in the previously uncharacterized gene F01D4.5--homologous with human TCF20 and RAI1--that suppresses the adverse phenotypes observed in m-tyrosine-treated tyrosine aminotransferase mutant C. elegans. To gain insights into the function of F01D4.5. RNA was isolated from N2 and F01D4.5(baf20) mutants and used for whole transcriptome profiling by RNA sequencing. Analysis of the data reveals a signficant reduction in the expression of ribos...
Source: GEO: Gene Expression Omnibus - June 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE115065 Epigenetic maintenance of topological domains in the rearranged gibbon genome
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Macaca mulatta ; Nomascus leucogenysThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Macaca mulatta Nomascus leucogenys Source Type: research

GSE71947 Pioneer transcription factor FoxA maintains an open nucleosome configuration for tissue-specific gene activation [MNase-Seq]
Contributors : Makiko Iwafuchi-Doi ; Greg Donahue ; Akshay Kakumanu ; Jason A Watts ; Shaun Mahony ; B F Pugh ; Dolim Lee ; Klaus H Kaestner ; Kenneth S ZaretSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusNuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal status of such open chromatin, e.g....
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE76517 Transcriptome responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes)
Contributors : Xu Wang ; Anna V Kukekova ; Andrew G ClarkSeries Type : Expression profiling by high throughput sequencingOrganism : Vulpes vulpesDomestication leads to a spectrum of striking behavioral changes whose genetic basis remains largely unknown. Silver foxes have been selectively bred for tame and aggressive behaviors for over 50 years at the Institute for Cytology and Genetics in Novosibirsk, Russia. To further understand the genetic basis and molecular mechanisms underlying tame and aggressive behavioral phenotypes segregating in selected strains of the silver fox, we quantified genome-wide gene expression level...
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Vulpes vulpes Source Type: research

GSE89568 Genome-wide gene-expression profile of mouse intestinal stem cells
Contributors : Omer H Yilmaz ; David M SabatiniSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this project is to generate transcriptome profiling of intestinal stem cells for a systemic analysis of cellular pathways involved in responses to fasting. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE97848 Deconstructive SCNT reveals heterogeneity within Treg population [bulk]
Contributors : Manching Ku ; Oktay Kirak ; Eugene KeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThymic-derived Treg cells consist of heterogeneous subsets with different characteristics and development. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE97849 Deconstructive SCNT reveals heterogeneity within Treg population [single-cell]
Contributors : Manching Ku ; Oktay Kirak ; Eugene KeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThymic-derived Treg cells consist of heterogeneous subsets with different characteristics and development. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE97850 Deconstructive SCNT reveals heterogeneity within Treg population
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE99456 Expression data from B6-sst1S and B6(WT) mouse bone-marrow derived macrophages
Contributors : Bidisha Bhattacharya ; Igor KramnikSeries Type : Expression profiling by arrayOrganism : Mus musculusUsing forward genetics in mice, we have identified a novel host resistance gene Ipr1, which mediates resistance to tuberculosis. We have shown that Ipr1-mediated pathway is regulated by IFNg in macrophages and plays an important role in resistance to several intracellular bacterial pathogens: Listeria, Francisella and Chlamydia. Functional studies of sst1 locus revealed that it plays a novel role in integrating signals generated by intracellular pathogens or viruses with mechanisms regulating activation, gene...
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE99562 Reprogramming of rabbit induced pluripotent stem cells toward Inner Cell Mass cells and chimeric competency with Kr üppel-like factors
In this study, we reprogrammed rbiPSCs using human Kr üppel-like factors (KLFs) 2 and 4 and cultured them in a medium supplemented with fetal calf serum and leukemia inhibitory factor. These cells (designated rbEKA) were propagated by enzymatic dissociation for at least 30 passages, during which they maintained a normal karyotype. This new culturing p rotocol resulted in transcriptional and epigenetic reconfiguration, as evidenced by the expression of transcription factors and histone marks associated with naïve pluripotency. Furthermore, microarray analysis of rbiPSCs, rbEKA cells, rabbit ICM cells, and rabbit e...
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Oryctolagus cuniculus Source Type: research

GSE101577 Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids (RNA-seq data set: 45d)
Contributors : Shan Bian ; Thomas R Burkard ; Zhenming Guo ; Juergen A KnoblichSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntroduction of brain tumor-relevant genetic aberrations initiates different subtypes of brain tumor-like neoplasms in cerebral organoids (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE101765 Genome-wide target profiling of pluripotency-associated long noncoding RNA Osclr8 by RAT-Seq
Contributors : Jifan Hu ; Zhonghua DuSeries Type : OtherOrganism : Mus musculusOsclr8 is a pluripotency-associated long noncoding RNA (lncRNA). Using RNA reverse transcription-associated trap sequencing (RAT-Seq), we profiled the genome-wide binding targets of Osclr8. This dataset will help study the mechanisms underlying the role of Osclr8 in the maintenance of pluripotency. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE103196 Gene expression changes after Ctcfl overexpression in NIH3T3 cells.
Contributors : Marek Bartkuhn ; Rainer Renkawitz ; Philipp BergmaierSeries Type : Expression profiling by arrayOrganism : Mus musculusThe two paralogous zinc finger factors CTCF and CTCFL differ in expression such that CTCF is ubiquitously expressed, whereas CTCFL is found during spermatogenesis and in some cancer types. Both factors share the highly conserved DNA binding domain and are bound to DNA sequences with an identical consensus. Here we analyzed the differential gene expression effect mediated by expression of Ctcfl in undifferentiated and differentiated NIH3T3 cell. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE103197 Gene expression changes after Ctcfl overexpression in undifferentiated and differentiated p19 cells.
Contributors : Marek Bartkuhn ; Rainer Renkawitz ; Philipp BergmaierSeries Type : Expression profiling by arrayOrganism : Mus musculusThe two paralogous zinc finger factors CTCF and CTCFL differ in expression such that CTCF is ubiquitously expressed, whereas CTCFL is found during spermatogenesis and in some cancer types. Both factors share the highly conserved DNA binding domain and are bound to DNA sequences with an identical consensus. Here we analyzed the differential gene expression effect mediated by expression of Ctcfl in undifferentiated and differentiated p19 cell. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE103198 Mapping of CTCF and CTCFL binding sites in 3T3 and p19 cells
Contributors : Marek Bartkuhn ; Rainer Renkawitz ; Philipp BergmaierSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusStudy of the differential binding behavior of the paralogous factors CTCF and CTCFL by ChIP-seq in mouse NIH3T3 and p19 cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

Gse103199 ctcfl
Series Type : Expression profiling by array ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE109087 Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii.
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by genome tiling arrayOrganism : Toxoplasma gondii ; Toxoplasma gondii ME49This SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by genome tiling array Toxoplasma gondii Toxoplasma gondii ME49 Source Type: research

GSE109842 Transcriptomes comparisons of Dhh KO, Ihh KO and Dhh/Ihh DKO ovaries
Contributors : Chang Liu ; Humphrey YaoSeries Type : Expression profiling by arrayOrganism : Mus musculusThe goal of the microarray analysis is to determine the redundant and distinct roles of Dhh and Ihh in ovarian functions (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE110610 Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids (RNA-seq data set: 130d)
Contributors : Shan Bian ; Thomas R Burkard ; Zhenming Guo ; Juergen A KnoblichSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntroduction of brain tumor-relevant genetic aberrations initiates different subtypes of brain tumor-like neoplasms in cerebral organoids (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE110611 Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids
Series Type : 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 - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE110987 Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death [ATAC-Seq]
Contributors : Renu Srivastava ; Zhaoxia Li ; Giulia Russo ; Jie Tang ; Ran Bi ; Usha Muppirala ; Sivanandan Chudalayandi ; Andrew Severin ; Mingze He ; Sam Vaitkevicius ; Carolyn Lawrence-Dill ; Peng Liu ; Ann Stapleton ; Diane Bassham ; Federica Brandizzi ; Stephen HowellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Zea maysNucleus was isolated from flash frozen from tunicamycin treated (0,6 and 12 hours) maize root samples, purified, then transposition reaction and and purification steps were carried out following the standard ATAC-seq protocol (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Zea mays Source Type: research

GSE111001 Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death [ChIP-Seq]
Contributors : Renu Srivastava ; Zhaoxia Li ; Giulia Russo ; Jie Tang ; Ran Bi ; Usha Muppirala ; Sivanandan Chudalayandi ; Andrew Severin ; Mingze He ; Sam Vaitkevicius ; Carolyn Lawrence-Dill ; Peng Liu ; Ann Stapleton ; Diane Bassham ; Federica Brandizzi ; Stephen HowellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Zea maysGFP-tagged nuclear localized versions of Zmbzip60& Zmbzip91 were overexpressed& pulled downed with GFP Ab to look for promoter binding elements (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Zea mays Source Type: research

GSE111250 Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death [RNA-Seq]
Contributors : Renu Srivastava ; Zhaoxia Li ; Giulia Russo ; Jie Tang ; Ran Bi ; Usha Muppirala ; Sivanandan Chudalayandi ; Andrew Severin ; Mingze He ; Sam Vaitkevicius ; Carolyn Lawrence-Dill ; Peng Liu ; Ann Stapleton ; Diane Bassham ; Federica Brandizzi ; Stephen HowellSeries Type : Expression profiling by high throughput sequencingOrganism : Zea maysWe tracked the gene expression events following treatment of maize seedlings with the endoplasmic reticulum (ER) stress agent tunicamycin. ER stress elicits the unfolded protein response (UPR) and when plants are faced with persistent stress, the UPR transitions from an ad...
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Zea mays Source Type: research

GSE111251 Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Zea maysThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Zea mays Source Type: research

GSE113194 Human ZNF341 deficiency underlies a recessive form of hyper IgE syndrome by disrupting STAT3 transcription-dependent STAT3 activity
We describe patients with an autosomal recessive form of HIES due to loss-of-function mutations of a previously uncharacterized gene, ZNF341. ZNF341 is a transcription factor that resides in the nucleus, where it binds a specific DNA motif present in various genes, including, most notably the STAT3 promoter. The patients ’ cells have low basal levels of STAT3 mRNA and protein. The auto-induction of STAT3 production, activation, and function by STAT3-activating cytokines is particularly strongly impaired. Like patients with STAT3 DN mutations, ZNF341-deficient patients lack Th17 cells, have an excess of Th2 cells, and...
Source: GEO: Gene Expression Omnibus - May 30, 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

GSE113232 Genome-wide analysis of gene expression upon BMI1 inhibition in human cortical neurons.
Contributors : Anthony Flamier ; Gilbert BernierSeries Type : Expression profiling by arrayOrganism : Homo sapiensStudy of gene expression regulated by BMI1 in human cortical neurons. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE114193 Mouse E14.5 Ret+ mechanoreceptors vs. laser captured spinal cord dorsal column midline cells
Contributors : Kim Kridsada ; Jingwen Niu ; Wenqin LuoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusOur study examined a population of radial glial-like cells (RGLCs) in the dorsal spinal cord midline that we showed provide long-distance growth support for longitudinal rapidly adapting (RA) mechanoreceptor axons during development of spinal cord dorsal column. To evaluate potential molecular markers of these cells, we isolated the RGLCs using hematoxylin and eosin staining to visualize the cell bodies in the dorsal column midline from E14.5 mouse embryos, and used laser capture micr...
Source: GEO: Gene Expression Omnibus - May 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research