GSE102730 C/EBP α overexpression overrides epigenetic reprogramming by RUNX1-ETO and RUNX1-EVI1 [RNA-seq]
Contributors : Justin Loke ; Paulynn S Chin ; Anna Pickin ; Peter Keane ; Salam A Assi ; Anetta Ptasinska ; Maria R Imperato ; Peter N Cockerill ; Constanze BoniferSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAcute myeloid leukemia (AML) is a heterogeneous disease caused by recurrent mutations in the transcription regulatory machinery. As a result, malignant myeloid cells display abnormal growth and are blocked in differentiation. One type of recurrent mutations affects RUNX1 which is subject to mutations and translocations, the latter giving rise to fusion proteins with aberrant t...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE102742 C/EBP α overexpression overrides epigenetic reprogramming by RUNX1-ETO and RUNX1-EVI1
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 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

GSE103050 Examination of tumor samples obtained after laparoscopic supracervical hysterectomy and a derivative leiomyosarcoma
Contributors : Carsten Holzmann ; Dirk Koczan ; Burkhard Helmke ; Joern BullerdiekSeries Type : Genome variation profiling by SNP array ; Expression profiling by arrayOrganism : Homo sapiensUnexpected malignant tumors are a rare finding after surgery for symptomatic leiomyomas but there is little doubt that morcellation of these lesions is associated with a higher risk of iatrogenic peritoneal spread compared to women having surgery without morcellation. Thus, the FDA has issued a warning against the use of power morcellation in the majority of women undergoing myomectomy or hysterectomy for treatment of fibroids.We presse...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array Expression profiling by array Homo sapiens Source Type: research

GSE103846 Transcriptome analysis of human embryonic stem cells (hESCs) upon siRNA-mediated knockdown of hESC-essential genes
Contributors : Atilgan Yilmaz ; Mordecai Peretz ; Nissim BenvenistySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe maintenance of pluripotency requires the coordinated expression of a set of essential genes. Thorough identification of these genes is vital for gaining a better understanding of the pluripotent state. To this end, we have recently generated a genome-wide loss-of-function library in haploid human pluripotent stem cells utilizing the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology using nearly 180,000 single guide RNAs (sgRN...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE103947 Fusion partner directed chromatin occupancy drives the transcriptome heterogeneity of MLL-fusion acute lymphoblastic leukemia
Contributors : Shan Lin ; Anetta Ptasinska ; Salam A Assi ; Constanze Bonifer ; James C MulloySeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensFusion of the N-terminus of the mixed-lineage-leukemia (MLL) gene with various partner genes drives acute lymphoblastic leukemia (ALL). Despite the fusion proteins sharing some common attributes, transcriptome heterogeneity of MLL-fusion ALL is observed and the underlying mechanism and biological consequences are unknown. We compared the genome-wide occupancy of MLL-Af4 and MLL-AF9 in human ALL cells expressing FLAG-tagged fusion p...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104551 RNA-Seq Analysis of Dose-Dependent TCDD-Elicited Femoral Gene Expression in Male Mice
Contributors : Kelly A Fader ; Rance Nault ; Timothy R ZacharewskiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDose-dependent femoral gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on gene expression in the femur of C57BL/6 male mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE104889 PFNF54-Pfs16-GFP-LUC gametocyte time course from commitment to maturity
Contributors : Ri ëtte A van Biljon ; Roelof D van Wyk ; Lindsey M Altenhofen ; Janette Reader ; Heather Painter ; Jandeli Niemand ; Manuel Llinás ; Lyn-Marié BirkholtzSeries Type : Expression profiling by arrayOrganism : Plasmodium falciparumPlasmodium falciparum gametocytes undergo 14 days of gametocytogenesis to generate mature, transmissible gametocytes. This timecourse delineates the transcriptional profiles of gametocytes from commitment to maturity. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Plasmodium falciparum Source Type: research

GSE105082 RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs
Contributors : Pierre Murat ; Giovanni Marsico ; Barbara Herdy ; Avazeh Ghanbarian ; Guillem Portella ; Shankar BalasubramanianSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensTranslational control is a key determinant of protein abundance, which in turns defines the physiology and pathology of human cells. Initiation of translation is highly regulated in eukaryotes and is considered as the rate-limiting step of protein synthesis. mRNA secondary structures in 5 ’ untranslated region (UTR) and associated helicases have been characterised as key determinants of translation ...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE105432 Whole-genome transcriptomic analysis of the cell fate switch induced by Notch activation in mouse mammary cells
Contributors : Silvia Fre ; Steffen RulandsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMice expressing the active form of Notch1(N1ICD) in the basal mammary epithelium (through SMAcreERT mice) were induced to express N1ICD at the onset of puberty (P24). This induces a cell fate switch that results in the acquisition of a luminal identity in the targeted cells. To understand the early signals responsible for this reprogramming of committed basal cells, we analysed by RNAseq the transcriptional changes occurring in the targeted cells after 72h of N1ICD expression. N1ICD-expressing c...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE106476 RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins
Contributors : Clemens Meyer ; Barbara Herdy ; Dhaval Varshney ; Giovanni Marsico ; Chris Taylor ; Clive D'Santos ; David Tannahill ; Shankar BalasubramanianSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensG-quadruplexes (rG4s) are recognized as key structures involved in RNA biology and are linked to neurodegenerative disease and cancer. However, detailed knowledge of rG4s and their binding partners is lacking. Here, a systematic, unbiased affinity proteomics approach identified 80 potential high-confidence interactors of the rG4 structure in the 5 ’UTR of the NRAS oncogene. Usi...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107962 MicroRNAs into body fluids from ten organs of mice exposed to cigarette smoke
Contributors : Alberto Izzotti ; Mariagrazia Longobardi ; Sebastiano La Maestra ; Rosanna T Micale ; Alessandra Pulliero ; Anna Camoirano ; Marta Geretto ; Francesco D'Agostini ; Rumen Balansky ; Mark Miller ; Vernon Steele ; Silvio De FloraSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiens ; Mus musculus ; Rattus norvegicusThe purpose of the present study was to validate the application of this epigenetic biomarker by using less invasive collection procedures.Using microarray analyses, we measured 1135 microRNAs in 10 organs and 3 body fluids of mice that were either unexposed or exposed to mainstream ...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Mus musculus Rattus norvegicus Source Type: research

GSE107965 Transcriptome analysis of human embryonic stem cells (hESCs) and human fibroblasts upon rapamycin
Contributors : Atilgan Yilmaz ; Mordecai Peretz ; Nissim BenvenistySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRapamycin inhibits mTORC1 complex in a variety of cells. We demonstrated that hESCs are more sensitive to rapamycin treatment as compared to somatic cells (BJ Fibroblasts) and also certain cancer cells (KBM7 cells). To study the molecular mechanisms of this disparity, we performed a transcriptome analysis (RNAseq) of rapamycin-treated hESCs and human fibroblasts for two time points (2 and 4 days of treatment). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108110 Long-acting immune responses including plasma cells and alteration of sebaceous glands cause atrophic scar formation in acne patients
Contributor : Johannes VoegelSeries Type : Expression profiling by arrayOrganism : Homo sapiensBackground: Possible outcomes of acne lesions are atrophic scars which may cause serious physical and psychological distress. Current treatments of post-acne scarring remain difficult and often require invasive procedures. Pathophysiological studies on acne scaring investigated only the first week of papule life. Objectives: Study the pathophysiology of atrophic acne scar formation to identify molecular and cellular pathways that can lead to new therapies for the prevention of acne scarring. Methods: Large-scale gene expression ...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE108290 Transcriptomic comparison between human epidermis and human sebaceous glands
Contributor : Johannes VoegelSeries Type : Expression profiling by arrayOrganism : Homo sapiensAnalysis of gene expression profiling of human epidermis and sebaceous glands. Skin samples were obtained from 5 healthy individuals undergoing plastic surgery (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE108864 Long noncoding RNA Hoxb3os is dysregulated in autosomal dominant polycystic kidney disease and regulates mTOR signaling
Contributors : K Aboudehen ; M D Gearhart ; P IgarashiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAutosomal dominant polycystic kidney disease (ADPKD) is a debilitating disease that is characterized by the accumulation of numerous fluid-filled cysts in the kidney. ADPKD is primarily caused by mutations in two genes, PKD1 and PKD2. Long noncoding RNAs (lncRNA) – defined by a length>200 nucleotides and absence of a long open reading frame – have recently emerged as epigenetic regulators of development and disease; however, their involvement in PKD has not been explore...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110616 Characterization of missense mutations in the tetratricopeptide region of O-GlcNAc transferase found in patients with X-linked intellectual disability
Contributors : Nithya Selvan ; Nripesh Prasad ; Shawn E Levy ; Lance WellsSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDfferential transcriptomics analysis of RUES-1 human embryonic stem cells edited using Crispr/Cas9 to contain four mutations in OGT found in certain patients with X-linked intellectual disability reveals changes in the gene expression profile associated with ectoderm and mesoderm development in all four mutant cell lines compared to the wild type control. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111309 DNAseq analysis of a genome-wide loss-of-function CRISPR/Cas9 library established in haploid human embryonic stem cells (hESCs)
Contributors : Atilgan Yilmaz ; Mordecai Peretz ; Nissim BenvenistySeries Type : OtherOrganism : Homo sapiensThe maintenance of pluripotency requires coordinated expression of a set of essential genes. Using our recently established haploid human pluripotent stem cells (hPSCs), we generated a genome-wide loss-of-function library targeting 18,166 protein-coding genes to define the essential genes in hPSCs. We could allude to an intrinsic bias of essentiality across cellular-compartments, uncover two opposing roles for tumor-suppressor genes, and link autosomal-recessive disorders with growth-retardation phenotypes to early ...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE111557 Expression data from surface airway epithelial basal cells, ciliated cells, and club cells.
Contributors : J F Engelhardt ; T J LynchSeries Type : Expression profiling by arrayOrganism : Mus musculusTo identify key genes that define surface airway epithelial (SAE) basal cells, we FACS isolated basal, ciliated, and club cell populations as previously reported (Zhao et al., 2014; PMID: 25043474) and performed microarray analysis on isolated mRNA. For fractionating SAE into basal, club, and ciliated populations, cells were stained with EpCAM-PECy7 (eBiosciences), GSI β4-FITC (Sigma), SSEA1-Alexa Fluor® 647 (BioLegend), and CD24-PE (BD Pharmingen) for 30 minutes on ice as previously described (Zhao et al., 2...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE111650 The effects of Lef-1 overexpression on culture-expanded MECs
Contributors : John F Engelhardt ; Thomas J LynchSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe mouse trachea is thought to contain two distinct stem cell compartments that contribute to airway repair —basal cells in the surface airway epithelium (SAE) and an unknown submucosal gland (SMG) cell type. Whether a lineage relationship exists between these two stem cell compartments remains unclear. Using lineage tracing of glandular myoepithelial cells (MECs), we demonstrate that MECs can give ris e to seven cell types of the SAE and SMGs following severe airway injury. ME...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111779 Quantitative Analysis of Follicular Helper T cell Transcriptomes from Wild Type and Apoe-/-
Contributors : Chung Yeonseok ; Ryu HeejuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to characterize the pathogenic features of follicular helper T cells (TFH cells) generated in atherogenic conditions by NGS-derived transcriptome profiling (RNA-seq).Methods: TFH cell mRNA profiles of 13-week-old wild type (WT) and Apoe knockout (Apoe-/-) mice were generated by deep sequencing, in duplicate, using Invitrogen mirVana miRNA Isolation Kit (Cat#AM1561). T...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111883 Transcriptomic analyses reveal genes with sexual dimorphic expression in the Arapaima gigas gonads and brain
Contributors : Carlos H Santos ; Vera M Almeida-Val ; Adalberto L ValSeries Type : Expression profiling by high throughput sequencingOrganism : Arapaima gigasPirarucu (Arapaima gigas, or A. gigas) is a native fish species to Amazon basin and, economically important in the Brazilian Amazonian for its great potential to aquaculture. In the natural environment the A. gigas is captured only in the sustainable development reserves of the State of Amazonas by applying a system of rotation in fishing in order to avoid overfishing of this important fishing resource. The reproductive biology of A. gigas has long been intriguing; ho...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arapaima gigas Source Type: research

GSE112473 Waveband Specific Transcriptional Control of Select Genetic Pathways in Xiphophorus maculatus Skin
Contributors : Ronald Walter ; Mikki Boswell ; Jordan Chang ; William Boswell ; Yuan Lu ; Kaela Novarro ; Sean Walter ; Dylan Walter ; Raquel Salinas ; Markita SavageSeries Type : Expression profiling by high throughput sequencingOrganism : Xiphophorus maculatusChanges in the transcriptional profiles of Xiphophorus maculatus skin was assessed by RNA-Seq after exposure to fluorescent (i.e., FL, 4,100K or “cool white”), or narrow wavelength regions of light between 300-600 nm (i.e., 50 nm or 10 nm regions, herein termed ”wavebands”). Exposure to varied 50 nm wavebands allowed identification of waveba...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Xiphophorus maculatus Source Type: research

GSE112658 Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation 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 - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113195 Sex differences in transcriptomic profiles in aged kidney cells of renin lineage
Contributors : Yuliang Wang ; Stuart J ShanklandSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRenin expressing cells in the kidney ’s juxta-glomeruluar compartment likely also serve as progenitors for adult glomerular cells in disease. Although these cells of renin lineage (CoRL) decrease in number with advancing kidney age, accompanied by less responsiveness to typical stimuli such as ACE-inhibition, mechanisms and the impac t of sex as a biological variable with age are not known. Accordingly, labeled CoRL were sorted from individual young (2m) and aged (27m) male and female...
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113287 Transcriptional profile in human S. haematobium infection (II)
Contributors : Lucja A Labuda ; Ayola A Adegnika ; Bruce A Rosa ; John Martin ; Makedonka Mitreva ; Maria YazdanbakhshSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGenome-wide transcriptional survey in peripheral blood mononuclear cells (PBMCs) by RNA-Seq in schoolchildren living in an endemic area in Gabon, with and without Schistosoma haematobium infection before and after treatment with the anthelminthic drug praziquantel. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113648 Quantitative whole transcriptomics sequencing of progeria-derived cells point to a key role of nucleotide metabolism in premature aging
Conclusions: Our study represents a detailed analysis of human PG lines transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell pathological line. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113660 UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Contributors : Wenan Chen ; John Easton ; Xiang ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSingle cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41. We also inlcude a bulk RNA-seq study of unsorted and sorted cells using CD44 as a marker (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100065 The differential expression of miRNA between murine glioma and PNET
Contributors : Sebastian Brandner ; Ningning LiSeries Type : Non-coding RNA profiling by arrayOrganism : Mus musculus ; synthetic constructmiRNA expression analysis of mouse glioma and PNET. Glioma was developed from SVZ cells through conditional codeletion of Pten/p53 or Rb/p53; while PNET was developed by codeletion of Rb/p53. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 29, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Mus musculus synthetic construct Source Type: research

GSE92314 Regulatory inversion in NAC networks steers the timing of age-dependent cell death in plants [RNA-Seq]
Contributors : Hyo-Jung Kim ; Ji-Hwan Park ; Jingil Kim ; Jung-Ju Kim ; Sung-Hyun Hong ; Jeongsik Kim ; Jinhee Kim ; Hye-Ryun Woo ; Pyung-Ok Lim ; Daehee Hwang ; Hong-Gil NamSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaAging is a time-dependent biological phenomenon governed by complex networks of regulatory components and their transitions over lifetime. Yet, there have been limited efforts to pin down age-associated networks and map their dynamic characteristics onto aging phenotypes. Here, we built time-course genetic regulatory networks of NAM/ATAF/CUC (NAC) transcripti...
Source: GEO: Gene Expression Omnibus - April 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE92369 Regulatory inversion in NAC networks steers the timing of age-dependent cell death in plants [Nanostring]
Contributors : Hyo-Jung Kim ; Ji-Hwan Park ; Jingil Kim ; Jung-Ju Kim ; Sung-Hyun Hong ; Jeongsik Kim ; Jinhee Kim ; Hye-Ryun Woo ; Pyung-Ok Lim ; Daehee Hwang ; Hong-Gil NamSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaAging is a time-dependent biological phenomenon governed by complex networks of regulatory components and their transitions over lifetime. Yet, there have been limited efforts to pin down age-associated networks and map their dynamic characteristics onto aging phenotypes. Here, we built time-course genetic regulatory networks of NAM/ATAF/CUC (NAC) transcription factors during the...
Source: GEO: Gene Expression Omnibus - April 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE92371 Regulatory inversion in NAC networks steers the timing of age-dependent cell death in plants
Series Type : Expression profiling by high throughput sequencing ; Expression profiling by arrayOrganism : Arabidopsis thalianaThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Expression profiling by array Arabidopsis thaliana Source Type: research

GSE113733 Next-generation sequencing analysis of chemically induced neurons from wild type (WT), Actb+/- (HET) and Actb-/- (KO) mouse embryonic fibroblasts (MEFs)
Conclusions: Our study shows that neuronal program induction was impaired in chemically induced neurons from Actb-/- mouse embryonic fibroblasts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 28, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE68361 Transcriptional profiling of CD1 mouse liver after 28 days and 90 days of daily administration of Phenobarbital in vivo
Contributors : Nina Ostenfeldt ; Michael R ömer ; Heidrun Ellinger-Ziegelbauer ; Dorthe B ThomsenSeries Type : Expression profiling by arrayOrganism : Mus musculusTo further our investigations for early biomarkers of non-genotoxic carcinogenesis, groups of mice were treated by gavage with a prototypic non-genotoxic carcinogen: Phenobarbital (PB, CAS: 57-30-7), for a period of 28 and 90d and liver tissue harvested for expression profiling. Control groups were treated with appropriate vehicle (0.5% Methylcellulose). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE68365 Transcriptional profiling of C57BL-mice with humanized CAR/PXR or CAR/PXR-knockout treated with DCB and CPA
Contributors : Colin Henderson ; Michael R ömer ; Rita Moreno ; Lynsey Chatham ; Amy Cameron ; Jennifer Grant ; Roland WolfSeries Type : Expression profiling by arrayOrganism : Mus musculusTo investigate the role of the nuclear receptors CAR (constitutive androstane receptor) and PXR (Pregnane X receptor) in mediating the effects of non-genotoxic carcinogens, groups of mice humanised or deleted for CAR and PXR were treated with 1,4-Dichlorobenzene or cyproterone acetate for 3d and liver tissue harvested for expression profiling. Control groups were treated with appropriate vehicles. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE68493 Transcriptional profiling of Primary Human Hepatocytes (PHH) depleted for CAR and treated with CITCO or Phenobarbital in -/+EGF medium
Contributors : Hugues de Boussac ; Michael R ömer ; Martine Daujat-ChavanieuSeries Type : Expression profiling by arrayOrganism : Homo sapiensIn primary human hepatocytes (PHH) the involvement of the Constitutive Androstane Receptor (CAR) in genes regulations has never been evaluated at the transcriptomic level. Here we investigated the impact of CAR depletion and epidermal growth factor on CAR dependent gene modulation in PHH. The xenosensor was activated by its direct (CITCO) or indirect (Phenobarbital/PB) agonists in presence or in absence of EGF. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE68495 Transcriptional profiling of Primary Human Hepatocytes (PHH) depleted for PXR and treated with CITCO or Phenobarbital in -/+EGF medium
Contributors : Hugues de Boussac ; Michael R ömer ; Martine Daujat-ChavanieuSeries Type : Expression profiling by arrayOrganism : Homo sapiensIn primary human hepatocytes (PHH) the involvement of the Pregnane X Receptor (PXR) in genes regulations by Phenobarbital (PB) has never been evaluated at the transcriptomic level. Here we investigated the impact of PXR depletion and epidermal growth factor on PXR dependent gene modulation by PB in PHH. The potential crosstalk with CAR was investigated using Phenobarbital and the direct CAR activator (CITCO) in presence or in absence of EGF. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE74424 Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models
In this study, genome-wide gene expression profiles of primary hepatocytes and liver sinusoidal endothelial cells (LSECs) were measured at day 12 for each cell culture system using Affymetrix GeneChips and analyzed via Gene Set Enrichment Analysis (GSEA). The culture systems analyzed include the commonly used collagen sandwich and monolayers of hepatocytes, as well as 3-dimensional (3D) engineered liver models that contain hepatocytes and LSECs (3DHL) and hepatocytes, LSECs, and Kupffer cells (3DHLK). Our results highlight the up-regulation of several hepatocyte specific functions in hepatocytes and a novel interplay betwe...
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE93675 Effect of ROQUIN2(Y691F) expression on mRNA levels upon BCR stimulation
Contributors : Roberto Bonasio ; Luca Busino ; Jaewoo ChoiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRoquin2, and its paralog Roquin1, are key regulator of mRNA decay. Roquin proteins recognize mRNAs containing a 3 ’-UTR stem-loop motif, called constitutive decay element (CDE), through the ROQ domain. Upon target engagement, Roquin proteins recruit the CCR4-CAF1-NOT complex, mediating mRNA deadenylation and destabilization. To study the effect of Roquin2 stabilization, we sought out to identify the relevant Roquin2 mRNA targets in human DLBCL. To this purpose, we measured d...
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE102665 PDGFRa+gp38+ mesenchymal cells in the peripheral tissues support terminal differentiation of ILC2 originated from fetal liver progenitor cells.
Contributors : Satoshi Koga ; Kazuyo MoroSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGroup 2 innate lymphoid cells (ILC2) are tissue-resident innate lymphocytes that are derived from common lymphoid progenitor (CLP). While specific progenitors and transcription factors essential for ILC2 differentiation have been well studied, external factors that regulate the commitment from CLP to ILC lineage, site that promote ILC2 terminal differentiation, and stromal cells that provide optimal microenvironment for ILC2 specific development are not fully understood. we demonstrated that the t...
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE103375 Metabolic and Transcriptional Alterations in the Early Stages of Cardiac Fuel Switch Hint at Novel mTOR-mediated Regulation of Hypertrophy
Contributors : Jonathan C Schisler ; Cam Patterson ; Rosalind A ColemanSeries Type : Expression profiling by array ; 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 - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE103376 Metabolic and Transcriptional Alterations in the Early Stages of Cardiac Fuel Switch Hint at Novel mTOR-mediated Regulation of Hypertrophy [Agilent Expression]
Conclusions- Short-term cardiac-specific ACSL1 inactivation (Acsl1H-/-) resulted in metabolic and transcriptional derangements distinct from those observed upon complete ACSL1 knockout, leading to the identification of novel mTORC1 targets that regulate cardiac hypertrophy development, and suggesting heart-specific mTOR signaling that occurs during the early stages of substrate switching. Moreover, the rate of increased glucose use correlated negatively with hypertrophy development, strongly suggesting that hearts do not become hypertrophied if they can compensate or switch faster from FA to glucose use. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE103811 MLL leukemia induction by t(9;11) chromosomal translocation in human hematopoietic stem cells using genome editing
Contributors : Johan Jeong ; Corina Schneidawind ; Michael L ClearySeries Type : Expression profiling by high throughput sequencing ; Genome variation profiling by high throughput sequencingOrganism : Homo sapiensGenome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks. However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development. Here we utilized TALENs to gener...
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome variation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE103863 Metabolic and Transcriptional Alterations in the Early Stages of Cardiac Fuel Switch Hint at Novel mTOR-mediated Regulation of Hypertrophy [RNA-seq]
Conclusions- Short-term cardiac-specific ACSL1 inactivation (Acsl1H-/-) resulted in metabolic and transcriptional derangements distinct from those observed upon complete ACSL1 knockout, leading to the identification of novel mTORC1 targets that regulate cardiac hypertrophy development, and suggesting heart-specific mTOR signaling that occurs during the early stages of substrate switching. Moreover, the rate of increased glucose use correlated negatively with hypertrophy development, strongly suggesting that hearts do not become hypertrophied if they can compensate or switch faster from FA to glucose use. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE104050 NUPR1 depletion activates premature senescence and overcomes tamoxifen resistance in breast cancer cells
ConclusionsCollectively, these findings suggest a critical role for NUPR1 as a transcriptional regulator that enables the drug persistence of breast cancers, thus providing a susceptible target to diagnose and treat drug resistance. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104850 Interrogating the functions of PRDM9 domains in meiosis
Contributors : Sarah Thibault-Sennett ; Qi Yu ; Fatima Smagulova ; Jeff Cloutier ; Kevin Brick ; Dan Camerini-Otero ; Galina V PetukhovaSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusHomologous recombination is required for proper segregation of homologous chromosomes during meiosis. It predominantly occurs at recombination hotspots that are defined by the DNA binding specificity of the PRDM9 protein. PRDM9 contains three domains which are typically different fa...
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Mus musculus Source Type: research

GSE106466 Single-cell RNAseq (SMART-seq2) of wild-type (TLAB) and MZoep (tz57) zebrafish embryos at 50% epiboly stage
Contributors : Jeffrey A Farrell ; Yiqun WangSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioSMART-seq2 was performed on single cells isolated from visually staged zebrafish embryos. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE106474 Drop-seq analysis of wild-type (TLAB) zebrafish embryos from high to 6-somite stage (12 timepoints)
Contributors : Jeffrey A Farrell ; Yiqun WangSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioWild-type zebrafish embryos were mechanically dissociated and profiled using Drop-seq (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE106587 Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Series Type : Expression profiling by high throughput sequencingOrganism : Danio rerioDuring embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-...
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE108457 Genetic dissection of the α-globin super-enhancer in vivo [RNA-seq]
Contributors : Deborah Hay ; Jim R Hughes ; Jelena Telenius ; Douglas R HiggsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMany genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. These super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements...
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE109775 Alterations in Sperm DNA Methylation, Non-coding RNA and Histone Retention Associate with DDT Induced Epigenetic Transgenerational Inheritance of Disease
This study was designed to investigate DDT induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to DDT during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Rattus norvegicus Source Type: research