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GSE104078 Role of small RNAs in gene dosage regulation in the ciliate Oxytricha trifallax
In conclusion, Oxytricha Dcl-1 and RdRP-dependent small RNAs that derive from the somatic nucleus contribute to the maintenance of gene dosage, possibly via a role in DNA replication , offering a novel role for these small RNAs in eukaryotes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Expression profiling by high throughput sequencing Other Oxytricha trifallax Source Type: research

GSE61955 Host transcriptome analysis of Aspergillus fumigatus infection in Airway Epithelial Cells
Contributors : Shernita L Lee ; Reinhard C LaubenbacherSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to determine the transcriptional response of primary normal human bronchial epithelial (NHBE) cells following interaction with A. fumigatus conidia at 2, 6, and 12 hours in order to examine the infection of airway epithelial cells at multiple time points of co-incubation. After total RNA isolation, the Illumina ® HiSeq 2000 next generation sequencing system was used to characterize the transcriptional response, in untreated and A. fumigatus exposed cells...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE74492 Glycosylation-related gene expression in the mucus-secreting gastrointestinal cell line HT29-MTX-E12 in response to infection by Helicobacter pylori
Contributors : Michael T Cairns ; Ananya Gupta ; Julie A Naughton ; Marian Kane ; Marguerite Clyne ; Lokesh JoshiSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe HT29 derivative cell line HT29-MTX-E12 (E12) produces an adherent mucus layer predominantly of the gastric MUC5AC mucin when grown on transwells. This mucus layer supports Helicobacter pylori survival in culture. E12 cells were infected with H. pylori and the transcriptome of infected and uninfected E12 were compared. Also included for comparison was the HT29 parent cell line grown on transwells.The study focused on glycosylation related genes...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE83602 Effect of vaccine administration routes on responses to a Bordetella pertussis outer membrane vesicle vaccine - lung
Contributors : Jeroen Pennings ; Ren é Raeven ; Jolanda BrummelmanSeries Type : Expression profiling by arrayOrganism : Mus musculusPulmonary immunization with an outer membrane vesicle pertussis vaccine led to improved protection and induction of a completely distinct immune response compared to subcutaneous administration.These adaptive responses were linked to early local and systemic signatures on the transcriptome level. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE83603 Effect of vaccine administration routes on responses to a Bordetella pertussis outer membrane vesicle vaccine - lymph nodes
Contributors : Jeroen Pennings ; Ren é Raeven ; Jolanda BrummelmanSeries Type : Expression profiling by arrayOrganism : Mus musculusPulmonary immunization with an outer membrane vesicle pertussis vaccine led to improved protection and induction of a completely distinct immune response compared to subcutaneous administration.These adaptive responses were linked to early local and systemic signatures on the transcriptome level. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE83604 Effect of vaccine administration routes on responses to a Bordetella pertussis outer membrane vesicle vaccine
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 - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE87174 Genome-wide expression patterns of microRNAs in ground state embryonic stem cells
We report that microRNAs are significantly differentially expressed when ESCs are cultured under different conditions, and that ground state pluripotency features a uniqure microRNA signature which is mainly encoded by microRNA-coding sequences within the developmentally important DLK1-Dio3 locus. Finally, we indicate that microRNA upregulated in ground state pluripotent cells (i.e. 2i/R2i) contribute to the maintenace of ground state pluripotency through stimulating self-renewal and inhibiting multi-lineague differentiation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Mus musculus Source Type: research

GSE87633 Organism-level analysis of vaccination reveals networks of protection across tissues
Contributors : Nicolas Chevrier ; Motohiko KadokiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWhole organs or CD8+ T cell populations sorted by FACS from tissues were isolated at various time points following vaccination with Vaccinia virus strain Modified Vaccinia Ankara (MVA; subcutaneously) and/or infection with strain Western Reserve (WR; intranasally). Total RNA was extracted from whole organs or sorted cell populations, RNA-seq libraries were prepared with a custom protocol, and sequenced at an average depth of ~5M/sample. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE89389 Novel data integration approaches identify concordant and discordant immune responses between mice and humans [mouse]
Contributors : Teresa Domaszewska ; Lisa Scheuermann ; Anca Dorhoi ; Karin Hahnke ; Hans Mollenkopf ; January WeinerSeries Type : Expression profiling by arrayOrganism : Mus musculusWe have conducted experiments to compare transcriptional response to tuberculosis (TB) in whole blood in two different TB murine models (susceptible 129S2 strain and resistant C57BL/6 strain) in time points day 1, day 7, day 14 and day 21 after infection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE89391 Novel data integration approaches identify concordant and discordant immune responses between mice and humans [human cells]
Contributors : Teresa Domaszewska ; Lisa Scheuermann ; Anca Dorhoi ; Karin Hahnke ; Hans Mollenkopf ; January WeinerSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe have conducted experiments to compare transcriptional response to tuberculosis (TB) in THP1 cells in time points 1hr,6hr and 24hr after infection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE89392 Novel data integration approaches identify concordant and discordant immune responses between mice and humans
Series Type : Expression profiling by arrayOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Mus musculus Source Type: research

GSE90697 Organism-level analysis of vaccination reveals networks of protection across tissues
Contributors : Nicolas Chevrier ; Motohiko KadokiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo study the response of single lung and liver memory CD8+ T cells to reactivation, mice vaccinated subcutaneously with MVA (10^7 PFUs/mouse) were subsequently challenged intranasally with: (1) PBS; (2) WR (10^7 PFUs/mouse); or (3) Vaccinia virus-derived B8R20-27 peptide (20 µg/mouse). Sixteen hours after challenge, single-cell suspensions were generated from lung or liver and lymphocytes were enriched using Percoll density centrifugation prior to immunostaining and cell sorting. Sin...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE93325 Proteogenomic characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling
Contributors : Jiheon Shin ; Minhyung Kim ; Hee-Jung Jung ; Hye L Cha ; Haeyoung Suh-Kim ; Sanghyun Ahn ; Jaehoon Jung ; YounAh Kim ; Yukyung Jun ; Sanghyuk Lee ; Daehee Hwang ; Jaesang KimSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHyperactivated mTOR signaling in the developing brain has been implicated in multiple forms of pathology including tuberous sclerosis complex (TSC).Here, we present an integrated analysis of transcriptomes and proteomes generated from wild-type and TSC1/Emx1-Cre forebrains.This led to comprehensive lists of genes and proteins whose expression levels we...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE95734 A somatic mutation in erythro-myeloid progenitors causes (late-onset) neurodegenerative disease
Contributors : Elvira Mass ; Alessandro Pastore ; Frederic GeissmannSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe pathophysiology of neurodegenerative diseases is poorly understood, and therapeutic options are few. Neurodegenerative diseases are hallmarked by progressive neuronal dysfunction and loss, associated with chronic glial and immune activation1. Microglia are the resident macrophages of the nervous system thought to be important for the clearance of debris after neuronal damage and aid to repair and regeneration. Their activation is viewed in general as a reactive proce...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE96099 3 ′ sequencing from human Huntington's disease and control motor cortex and cerebellum.
We report 11% of genes from Huntington's disease patient motor cortex exhibit a change in at least one of their 3 ′UTR isoforms, commensurate with the 11% of genes which show different total expression in HD motor cortex versus control. In contrast, gene isoform and expression changes are minimal ( (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Mus musculus Source Type: research

GSE96908 Genome-wide Analysis of Binding Sites of the Caenorhabditis elegans NR4A Nuclear Receptor NHR-6 During Spermatheca Organogenesis
Contributors : Chris R Gissendanner ; Brandon PraslickaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Caenorhabditis elegansThe gene nhr-6 encodes the sole C. elegans NR4A nuclear receptor homolog which has a critical role in organogenesis by regulating the development of the spermatheca organ. Here we utilized chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to identify NHR-6 binding sites during both the late L3/early L4 and mid L4 developmental stages. Our results revealed 30,745 enriched binding sites for NHR-6 with sites specific to each developm...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE97007 Investigation of the Molecular Action of Actinorhodin
Contributors : Stefanie Mak ; Justin R NodwellSeries Type : Expression profiling by high throughput sequencingOrganism : Staphylococcus aureusActinorhodin is a blue-pigmented, redox-active pigmented secondary metabolite that is produced by the bacterium Streptomyces coelicolor. Although actinorhodin has been used as a model compound for studying secondary metabolism, its mechanism is not well understood. In this work, we have conducted a comprehensive chemical genetic investigation of actinorhodin ’s antibacterial effect on target organisms. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Staphylococcus aureus Source Type: research

GSE97184 Intestinal epithelial and intraepithelial T cell crosstalk mediates a dynamic response to infection
Contributors : David P Hoytema van Konijnenburg ; Bernardo S Reis ; Virginia Pedicord ; Julia Farache ; Gabriel Victora ; Daniel MucidaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusOral infection of mice with Salmonella Typhimurium leads to rapid changes in small intestinal TCRgd IEL behavior. How these changes are induced is currently unknown. By analyzing the transcriptome of TCRgd and intestinal epithelial cells in the steady state and after infection, we find a potential role for epithelial cell MYD88 expression in regulating the IEL response. By additionally analyzing the trans...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE100118 Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing [RNA-seq]
Contributors : Kathy Niakan ; Paul Blakeley ; Norah M FogartySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDespite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR?Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. Using the...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100119 Genome editing reveals a role for OCT4 in human preimplantation development [MiSeq]
Contributors : Norah Fogarty ; Afshan McCarthy ; Paul Blakeley ; Kathy NiakanSeries Type : OtherOrganism : Homo sapiens ; Mus musculusDespite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR?Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. Using these refined met...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Other Homo sapiens Mus musculus Source Type: research

GSE100120 Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing
Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Mus musculus Source Type: research

GSE100136 Analysis of temporal lens gene expression microarrays to expand the eye gene discovery tool iSyTE
Conclusions: The updated iSyTE web-interface: (1) comprehensively informs on normal lens developmental and cataract-associated transcriptome dynamics and identifies new high-priority candidates for these processes, and (2) offers user-friendly visualization. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE101487 A Distinct Population of Thirst-Associated Preoptic Neurons Encodes an Aversive Motivational Drive
Contributors : William Allen ; Liqun LuoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe FACS-isolated single thirst-associated neurons from the median preoptic hypothalamus of mice and determined their individual transcriptomes. This characterization revealed a molecularly distinct population of excitatory thirst-associated neurons that is responsible for producing thirst motivational dirve. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE102639 RNA seq_A375 gSMARCB1 + A549 etoposide, Aurora kinases inhibitors treated
Contributors : Liqin Wang ; Iris de Rink ; Cor LieftinkSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo study the senescence gene signatures in the cells, which were genetic SMARCB1 depleted or treated with aurora kinase inhibitors or etoposide, we performed next generation RNA sequencing on these cell, and 'FRIDMAN_SENESCENCE_UP' geneset was used to determine the enrichment of senescence-related genes. The RNA sequencing results include (1) A375 cells and SMARCB1 depleted counterparts. (2) A549 cells and aurora kinase inhibitor (Alisertib, barasertib or tozasertib) or etoposide tre...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE102982 JNK activation of BIM promotes hepatic oxidative stress, steatosis and insulin resistance in obesity
Contributors : Esteban N Gurzov ; Jean-Valery TuratsinzeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe BCL-2 family are crucial regulators of the mitochondrial pathway of apoptosis in normal physiology and disease. Besides their role in cell death, BCL-2 proteins have been implicated in the regulation of mitochondrial oxidative phosphorylation and cellular metabolism. However, it remains unclear whether these proteins have a physiological role in glucose homeostasis and metabolism in vivo. Here we report that fat accumulation in the liver increases JNK-dependent BIM expression in...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE103364 Streptococcus pneumoniae TIGR4 phase-locked opacity variants differ in virulence phenotypes
Contributors : Melissa B Oliver ; Ankita Basu Roy ; W E SwordsSeries Type : Expression profiling by high throughput sequencingOrganism : Streptococcus pneumoniaeStreptococcus pneumoniae (pneumococcus) is a leading human pathogen that can cause serious localized and invasive diseases. Pneumococci can undergo a spontaneous and reversible phase variation that is reflected in colony opacity, which allows the population to adapt to different host environments. Generally, transparent variants are adapted for nasopharyngeal colonization whereas opaque variants are associated with invasive disease. In recent work, colony phase var...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Streptococcus pneumoniae Source Type: research

GSE103982 Bach2 promotes B cell receptor-induced proliferation of B lymphocytes and represses cyclin-dependent kinase inhibitors
In this study, we demonstrate that Bach2 is required to sustain high levels of B cell proliferation in response to BCR signaling. Following BCR engagement in vitro, B cells from Bach2-deficient (Bach2-/-) mice showed lower incorporation of 5-bromo-2'-deoxyuridine (BrdU) and reduced cell cycle progression compared with wild-type (WT) cells. Bach2-/- B cells also underwent increased apoptosis as evidenced by an elevated frequency of sub-G1 cells and early apoptotic cells. Transcriptome analysis of BCR-engaged B cells from Bach2-/- mice revealed reduced expression of the anti-apoptotic gene Bcl2l1 encoding Bcl-XL, and an elev...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104018 RNAseq of T-ALL upon long non coding rna purturbation
Contributors : Iannis Aifantis ; Yixiao Gong ; Yoon S YapSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensT cell leukemia cell lines transciptome changes upon long non coding RNA knockdown by CRISPR and ASO. The target lncRNA is a novel lncRNA called "lnrCXCR4". The sequence of this lncRNA is available at the foot of this page. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104031 Evaluation of animal models of AD
This study was designed to measure expressional profile of genes from brain tissues of animal models of AD. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104032 Expression data from PEG-GNRs treated cells
Contributor : Hongyuan SongSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe used microarrays to detail the global programme of gene expression treated with PEG-GNRs and identified distinct classes of up-regulated and down-regulated genes during this process. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104052 N-methyl-D-aspartate receptors mediate activity-dependent down-regulation of potassium channel genes during the expression of homeostatic intrinsic plasticity
Contributors : KwanYoung Lee ; Sara E Royston ; Max O Vest ; Daniel J Ley ; Seungbae Lee ; Eric C Bolton ; HeeJung ChungSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusUsing whole-cell patch clamp recording and unbiased gene expression profiling in rat dissociated hippocampal neurons cultured at high density, we demonstrate here that chronic activity blockade induced by the sodium channel blocker tetrodotoxin leads to a homeostatic increase in action potential firing and down-regulation of potassium channel genes. In addition, chronic activity blockade reduces total potassium current, as well as prot...
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE104068 Genome-wide analysis of changes in gene expression induced by Eph and ephrin stimulation of mouse neural progenitors
Contributor : Alice DavySeries Type : Expression profiling by arrayOrganism : Mus musculusThe hypothesis tested in the present study was that activation of Eph or ephrin signaling in neural progenitors induces a transcriptional response which participate in the control of progenitor self-renewal. Results provide important information on transcriptional changes in response to activation of Eph receptors. They also show that activation of ephrin signaling does not induce a transcriptional response at genome-wide level. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104076 Determination of trastuzumab responsive microRNAs in SKBR3 and BT474 cells.
Contributors : Emine E Cilek ; Bala G DedeogluSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensTo develop gene-miRNA and pathway-miRNA networks in trastuzumab treatment, we performed a recent miRNA microarray profiling in trastuzumab treated/untreated SKBR3 and BT474 cell lines.The cells were plated at a starting density of 2 millions in 100 mm cell culture dishes and then, they were treated with 6 ug/mL trastuzumab and PBS in two replicates. Total RNA was isolated with the TRIzol reagent (Invitrogen) according to the manufacturer's instructions. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 21, 2017 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE104026 The presence of satellite RNA exacerbates symptoms and transcriptomic response of Nicotiana benthamiana during peanut stunt virus infection
In this study we elucidated the plant response to PSV-G strain which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA which causes exacerbation of pathogenesis in Nicotiana benthamiana. In order to study plant response to PSV infection and to explain mechanisms underlying symptoms exacerbation caused by satRNA we did transcriptome profiling of N. benthamiana challenged by PSV with/ without satRNA using species-specific microarrays. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Nicotiana benthamiana Source Type: research

GSE98314 Melanoma cell lines treated with dabrafenib ± trametinib
Contributors : Helen Rizos ; Gulietta PupoSeries Type : Expression profiling by arrayOrganism : Homo sapiensRapid resistance to BRAF inhibitors in BRAFV600-mutant metastatic melanoma has produced an urgent need for new treatment options. BRAF inhibitor resistance commonly involves reactivation of mitogen-activated protein kinase (MAPK) signaling and yet inhibition of downstream kinases has not circumvented resistance, partly because MAPK is regulated via a complex network of feedback mechanisms that influence pathway rebound. To examine the transcriptome responses of melanoma cells to MAPK inhibition, a panel of 11 BRAFV60...
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE99798 Meg3 binding sites in mouse insulinoma cells
Contributors : Sucharitha Iyer ; Sunita AgarwalSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe have shown that increased β-cell proliferation in functioning pancreatic neuroendocrine tumors (insulinomas) correlated with reduced expression of the long non-coding RNA Meg3 and increased expression of the oncogenic receptor c-Met. To investigate the target binding sites of Meg3 in and around the c-Met gene, we did ChIRP- Seq using biotinylated probes from the mouse Meg3 RNA sequence. This would help us better understand how Meg3 regulates ithe expression of c-Met to ...
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE102608 Response of Phaeocystis antarctica under changing iron conditions
Contributors : Mariam R Rizkallah ; Stephan Frickenhaus ; Lars Harms ; Klaus Valentin ; Ahmed Moustafa ; Sara BeszteriSeries Type : Expression profiling by high throughput sequencingOrganism : Phaeocystis antarcticaThe study aims at deciphering the response of Phaeocystis antarctica under iron limitation and iron supplementation at a transcriptomic level. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Phaeocystis antarctica Source Type: research

GSE103547 Defining the developmental stage of human podocytes in kidney organoids derived from pluripotent stem cells
Contributors : Benjamin S Freedman ; Yuliang WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensA critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC-podocytes) have recently been generated in nephron-like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here we show that hPSC-podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recap...
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE103981 P68 protein inhibited the growth and invasion of glioma cells by adjusting the DUSP5
In this study, gene chip was used to search for new downstream genes DUSP5 that affect the growth of glioma.The expression of inhibition or overexpression of P68 protein in glioma cell lines was consistent with the expression of expression DUSP5 and the effect of reduction DUSP5 on the growth of the tumor.The ability of the tumor to recover after the expression of DUSP5 expression in glioma cells was reduced,This indicates that P68 regulates the growth, increment and invasion of glioma cells.Through affymetrix gene chip, we use 3 biological specimens.That is three SIP68 , control of the glioma cells that infect NC.Try to g...
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE103985 Comprehensive understanding of identities and antigenicities of surface and secreted proteins in Toxoplasma gondii tachyzoites
This study comprehensively revealed the identities and antigenicities of T. gondii surface and secreted proteins, which laid foundation for further screening new T. gondii antigens, developing immunological diagnosis methods, and studying host immune response to T. gondii infection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE103989 Gene expression profiling in LoVo-P compared with LoVo-C cells
Contributors : Zhonghua Chu ; Qiusheng LanSeries Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensThe differential expression of mRNA in LoVo-P cells compared with LoVo-C cells was successfully detected using the Arraystar Human LncRNA/mRNAArray V4.0, that used for the global profiling of 20730 human mRNA and 40173 long non-coding RNA (LncRNA) transcripts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE103992 Gene expression assessed by genome wide hybridization bead array in T84 polarized tight monolayers after challenge with celiac disease-associated bacteria [CTR 32 33 34]
Contributors : Marie-Louise Hammarstr öm ; Grzegorz PietzSeries Type : Expression profiling by arrayOrganism : Homo sapiensAnalysis of the influence of celiac disease-associated bacteria on intestinal epithelial cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE103997 Impeding transcription of expanded microsatellite repeats by deactivated Cas9
Contributors : Belinda S Pinto ; Tanvi Saxena ; Ruan Oliveira ; Hector R Mendez-Gomez ; John D Cleary ; Lance T Denes ; Ona McConnell ; Juan Arboleda ; Guangbin Xia ; Maurice Swanson ; Eric T WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTranscription of expanded microsatellite repeats is associated with multiple human diseases, including myotonic dystrophy, Fuchs ’ endothelial corneal dystrophy, and C9orf72-ALS/FTD. Eliminating or reducing production of RNA and proteins arising from these expanded loci holds therapeutic benefit. Here, we tested the hypothesis that a deact...
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104012 H. salinarum R1 wildtype vs cyc-
Contributors : Walter J Muller ; Melinda D Capes ; Shiladitya DasSarma ; Esta van Heerden ; Martha S SmitSeries Type : Expression profiling by arrayOrganism : Halobacterium salinarum ; Halobacterium salinarum NRC-1Investigating the possible physiological role of CYP174A1 (cyc) in H. salinarum (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 20, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Halobacterium salinarum Halobacterium salinarum NRC-1 Source Type: research

GSE103943 Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae
Contributors : Daniel Rossbach ; Robert Sclafani ; D S Bryan ; Jay HesselberthSeries Type : OtherOrganism : Saccharomyces cerevisiaeCdc7 kinase is known to initiate DNA replication, but it is unknown where Cdc7 is found within the genome. We modified the Calling Cards method that uses the Ty5 retrotransposon to investigate Cdc7 binding in the genome. The Ty5 retrotransposon is inserted into the genome by DNA transcription factors or replication factors binding within the genome. We find that Cdc7 inserts Ty5 transposons throughout chromosomes and furthermore creates more Ty5 insertions into regions of DNA that are known to...
Source: GEO: Gene Expression Omnibus - September 19, 2017 Category: Genetics & Stem Cells Tags: Other Saccharomyces cerevisiae Source Type: research

GSE61572 Cystatin C modulates the release of inflammatory cytokines in Lipopolysaccharide-activated monocytes
Contributors : Susanne T Gren ; Sabina Janciauskiene ; Danny Jonigk ; Peter H Kvist ; Thomas B Rasmussen ; Jens G Gerwien ; Katarina H åkansson ; Olof GripSeries Type : Expression profiling by arrayOrganism : Homo sapiensCystation modulates expression of inflammatory cytkines in LPS activated monocytes (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 18, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE76710 Inferring gene regulatory networks that control maintenance and identity of the Arabidopsis root stem cells
Contributors : Barbara Muller ; Rosangela SozzaniSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaWe isolated QC and xylem cells by sorting GFP+ cells marked with pWOX5::GFP and pTMO5::GFP respectively.We obtained cell-type specific transcriptional profiles of QC and xylem cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 18, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE79253 BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [RNA-seq]
Contributors : Georg E Winter ; Dennis L Buckley ; Michael A Erb ; James E BradnerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer arises from the malignant interplay between oncogenic signaling and cell specification. Transcriptionally activated stem, growth and survival programs reshape an epigenomic identity defined by a transcriptional core regulatory circuitry. To study and disrupt oncogenic transcription, we first created inhibitors of BET bromodomains. Selective antagonism of oncogenic transcriptional signaling arises from bromodomain-specific activity. Recently, we innov...
Source: GEO: Gene Expression Omnibus - September 18, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE79271 BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [NET-seq]
Contributors : Georg E Winter ; Dennis L Buckley ; James E BradnerSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensCancer arises from the malignant interplay between oncogenic signaling and cell specification. Transcriptionally activated stem, growth and survival programs reshape an epigenomic identity defined by a transcriptional core regulatory circuitry. To study and disrupt oncogenic transcription, we first created inhibitors of BET bromodomains. Selective antagonism of oncogenic transcriptional signaling arises from bromodomain-specific activity. Recently, we innovated a s...
Source: GEO: Gene Expression Omnibus - September 18, 2017 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE79288 BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [ChIP-seq]
Contributors : Georg E Winter ; Dennis L Buckley ; Michael A Erb ; James E BradnerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensCancer arises from the malignant interplay between oncogenic signaling and cell specification. Transcriptionally activated stem, growth and survival programs reshape an epigenomic identity defined by a transcriptional core regulatory circuitry. To study and disrupt oncogenic transcription, we first created inhibitors of BET bromodomains. Selective antagonism of oncogenic transcriptional signaling arises from bromodomain-specific activity. Rece...
Source: GEO: Gene Expression Omnibus - September 18, 2017 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research