GSE143839 Maternal reprogramming of histone methylation regulates germline versus somatic cell fates
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Caenorhabditis elegansThis SuperSeries is composed of the SubSeries listed below.
55m
Contributors : Junko Murai ; Yves PommierSeries Type : Expression profiling by arrayOrganism : Homo sapiensSchlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin. Concomitantly SLFN11 selectively activates cellular stress response...
55m
Contributors : Brandon S Carpenter ; Teresa W Lee ; Caroline F Plott ; Jovan S Brockett ; Dexter A Myrick ; David J KatzSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Caenorhabditis elegansIn C. elegans, the H3K4me2 demethylase, SPR-5, and the H3K9 methyltransferase, MET-2, are maternally deposited into the oocyte where they reprogram histone methylation to prevent somatic expression of germline genes. Here, we show that the progeny of spr-5; met-2 mutants...
55m
Contributors : Lorinc Pongor ; Hongliang Zhang ; Junko Murai ; Yves PommierSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensSchlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin....
55m
Contributors : Brandon S Carpenter ; Teresa W Lee ; Caroline F Plott ; Jovan S Brockett ; Dexter A Myrick ; David J KatzSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansIn C. elegans, the H3K4me2 demethylase, SPR-5, and the H3K9 methyltransferase, MET-2, are maternally deposited into the oocyte where they reprogram histone methylation to prevent somatic expression of germline genes. Here, we show that the progeny of spr-5; met-2 mutants display a severe...
55m
Series Type : Expression profiling by array ; Methylation profiling by genome tiling arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
55m
Contributors : Violeta Chitu ; Ping Wang ; Deyou Zheng ; E R StanleySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusALSP is a CSF1R-deficiency dementia associated with increased CSF2 expressionMonoallelic deletion of Csf2 rescues most behavioral deficits and histopathological changes in Csf1r+/- mice by preventing microgliosis and eliminating most microglial transcriptomic alterations, including those indicative of oxidative stress and demyelinationElevation...
55m
Contributors : Lorinc Pongor ; Junko Murai ; Yves PommierSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSchlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin. Concomitantly SLFN11 selectively...
55m
Contributors : Naohiko Seki ; Reona OkadaSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo identify differentially expressed genes by specific gene silencing (via siRNAs or knockout) in human cancer, several cell lines (esophageal cancer and gastric cancer) were subjected to Agilent whole genome microarrays.
55m
Contributors : Lorinc Pongor ; Junko Murai ; Hongliang Zhang ; Yves PommierSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensSchlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin....
55m
Contributors : W van Leeuwen ; A Aguilera-Gomez ; C RabouilleSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterThe phase separation of the non-membrane bound Sec bodies occurs in Drosophila S2 cells by coalescence of components of the ER exit sites under the stress of amino-acid starvation. Here we provide the comparison of the gene expression profiles of S2 cells grown in full medium (Schneider's) and S2 cells upon of amino-acid starvation in KRB
55m
Contributors : Francesca Odoardi ; Moritz HermannSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusWe report the expression profile of beta-synuclein reactive CD4+ T cells isolated from blood and brain in animals affected by Experimental autoimmune encephalomyelitis
55m
Contributors : Alexander Wallenstein ; Ulrich DobrindtSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Escherichia coliBy comparing the transcriptome profile upon deletion or overexpression of ClbR or ClbQ, we addressed the role of these proteins in regulation of colibactin expression. Our global screen indicates that ClbR is the key transcriptional activator of colibactin expression. In addition, we further investigated potential transcription start sites of the...
55m
Contributor : Sandra SchmitzSeries Type : Expression profiling by genome tiling arrayOrganism : Homo sapiensTo investigate if cetuximab induces epithelial to mesenchymal transition (EMT) and activation of cancer associated fibroblast (CAF) in the tumors of patients with squamous cell carcinoma of the head and neck (SCCHN).Cetuximab was administered for two weeks prior to surgery to 20 treatment-naïve patients (CHIRON study). Five untreated patients were included as controls. Tumor biopsies were...
55m
Contributors : Sarah Forrester ; Amy Goundry ; Bruna Torres Dias ; Thyago Leal Calvo ; Milton Osório Moraes ; Paul M Kaye ; Jeremy C Mottram ; Ana C de Araújo LimaSeries Type : Expression profiling by high throughput sequencingOrganism : Leishmania donovani ; Leishmania infantum ; Mus musculusFIve 6/8 week old female BALB/c mice were infected with the LV9 L. donovani strain,five mice were infected with the L. infantum NCL strain, five were uninfected, and spleen and liver were taken from mice...
55m
Contributors : Elisa Barbieri ; Connor Hill ; Mathieu Quesnel-Vallieres ; Yoseph Barash ; Alessandro GardiniSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe developed a new method to profile nascent RNA in mammalian cells. The new methodology is based on the incorporation of thio-UTP, an analog of UTP, during in vitro RNA Polymerase run-on.
55m
Contributors : Zhong Yao ; Xingang LiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGlioblastoma multiforme (GBM) is the deadliest form of brain tumor with a median survival time of 15 months due to drug resistance. Ursodeoxycholic acid (UDCA) is approved of cancer suppressive potential in several tumors. Here we researched on the antitumor potential of UDCA on GBM. The CCK-8 and colony formation was used for detecting cell viability. RNA sequencing hinted...
55m
Contributors : Lorinc Pongor ; Junko Murai ; Yves PommierSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSchlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin. Concomitantly SLFN11 selectively...
55m
Contributors : Orçun Haçariz ; Charles Viau ; Jianguo XiaSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansRNAseq was carried out to compare the gene expression profiles of the worms grown with individual bacteria to understand the bacterial effect
55m
Contributors : Lorinc Pongor ; Junko Murai ; Hongliang Zhang ; Yves PommierSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensSchlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin....
55m
Contributors : Hanan S Elsarraj ; Yan Hong ; Jeffrey Thompson ; Fariba BehbodSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThere is limited research on which specific Wnt targets are regulated by B-Cell Lymphoma-9 (BCL9) and whether BCL9 regulates other signaling pathways to drive cancer malignancy. Here we demonstrated that BCL9 drives DCIS invasive progression by regulation of genes involved in cellular growth, invasion and migration.
55m
Contributors : Lorinc Pongor ; Junko Murai ; Yves PommierSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensSchlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin. Concomitantly...
55m
Contributors : Shanshan Song ; Stefan Timm ; Steffen N Linder ; Viktoria Reimann ; Wolfgang R Hess ; Martin Hagemann ; Eva-Maria BrouwerSeries Type : Expression profiling by arrayOrganism : Synechocystis sp. PCC 6803The introduction of alternative CO2-fixing pathways such as formate synthesis and assimilation may improve the efficiency of biological carbon fixation that appears to be limited by the enzymatic properties of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we aimed...
55m
Contributors : Suyu Quan ; Xuemei NanSeries Type : Expression profiling by high throughput sequencingOrganism : Bos taurus ; Ovis ariesMilk can mediate maternal-neonatal signal transmission by the bioactive component-extracellular vesicles (EVs), which select specific types of miRNA to encapsulate. The miRNA profiling of sheep milk EVs was characterized by sequencing and compared with that of cow milk. Sheep milk EVs contained various small RNAs, including tRNA, Cis-regulatory element, rRNA, snRNA,...
55m
Contributors : Carlos Villacorta-Martin ; Augusto VillanuevaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe purpose of this experiment is to detect and characterize heterogeneity in single cell sequence data from liver cancer
55m
Contributors : Zhirong Li ; Yipeng Wu ; Cong Zhang ; Suli Dai ; Lianmei Zhao ; Baoen ShanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLong noncoding RNAs (lncRNAs) are emerging as important regulators in cellular processes. In the present study, the effects of the long non-coding RNA, SNHG5 was investigated in lung adenocarcinoma (LAD) and we also revealed the underlying mechanisms of it. Overexpressed SNHG5 suppressed migration and invasion of LAD...
55m
Contributor : Elana FertigSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensDNA methylation arrays for 8 Surgical specimens(DNA extracted from FFPE slides) after cetuximab treatment
55m
Contributors : Keiichiro Kizaki ; Yo-Han KimSeries Type : Expression profiling by arrayOrganism : Bos taurusWe investigated changes in rumen fermentation, peripheral blood metabolites and hormones, and hepatic transcriptomic dynamics in Holstein cows with and those without subacute ruminal acidosis (SARA) during the periparturient period.
55m
Contributors : Reshef Tal ; Shafiq Shaikh ; Ying Liu ; Nicola Pluchino ; Harvey Kliman ; Myles H Alderman ; Jehanzeb Kayani ; Ramanaiah Mammillapalli ; Hugh S TaylorSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBone marrow (BM)-derived progenitor cells (BMDPCs) are known to migrate and give rise to endometrial cells however their functional contribution to implantation and pregnancy are unknown . Here we show that implantation and pregnancy are strong...
55m
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
55m
Contributors : Guoxu Song ; Yong TianSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe neurodegenerative disease spinocerebellar ataxia type 3 (SCA3; also called Machado-Joseph disease, MJD) is a trinucleotide repeat disorder caused by expansion of CAG repeats which encoding an abnormal long polyglutamine (polyQ) tract in ataxin-3 of the ATXN3 gene. Even now the pathogenic mechanism has remained elusive and no cure method is currently available.In this study, we first applied...
55m
Contributor : Yunbao PanSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiens ; synthetic constructWe select 3 pairs of tissue samples, including 3 breast tissues and 3 adjacent tissues, and then perform miRNA chip detection to find differential miRNAs.We used microarrays to identify differential expressed miRNAs in breast cancer and paired normal breast tissue
3h
Contributor : Kimberly StegmaierSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTargeted therapy studies with small molecules against kinases, such as spleen tyrosine kinase (SYK), are underway in patients with acute myeloid leukemia (AML) and show promising initial results. Identifying the potential mechanism of resistance and finding new drug combinations to overcome them, however, is essential for the long-term success of these targeted agents. Here, we...
8h
Contributors : K G Sanchez ; M G Ferrell ; A G Chirakos ; K G Nicholson ; R G Abramovitch ; M G Champion ; P G ChampionSeries Type : Expression profiling by high throughput sequencingOrganism : Mycobacterium marinumRegulation of M. marinum gene expression in an espM deletion strain
10h
Contributors : Ashish Jain ; Jiude Mao ; R. M Roberts ; Geetu Tuteja ; Cheryl RosenfeldSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusC57BL6J mice were fed 200ug/kg body weight BPA or BPS for two weeks and then bred. Placenta tissue was collected at embryonic day 12.5, and dams received checmicals until this day. RNA-Seq was carried out on placenta tissue, and 13 genes were identified to have altered expression to a similar extent in BPA and BPS treated...
11h
Contributors : Alicia N Vagnozzi ; Polyxeni PhilippidouSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study was to identify potential Hox5 target genes in cervical motor neurons (C3-C6) using unbiased genomic screens (RNA-seq). We examined expression changes independently of motor neuron cell death by deleting the pro-apoptotic gene Bax in both control and experimental mice.
12h
Contributors : Eleftheria Karanika ; Katerina Soupsana ; Anastasia Christogianni ; Dimitris Stellas ; Apostolos Klinakis ; Anastasia S Politou ; Spyros GeorgatosSeries Type : Expression profiling by arrayOrganism : Mus musculusThe kinase Haspin phosphorylates histone H3 at threonine-3 (H3T3ph), creating a docking site for the Chromosomal Passenger Complex (CPC). CPC plays a pivotal role in preventing chromosome misalignment. Here, we have examined the effects of 5-Iodotubercidin (5-ITu), a...
13h
Contributors : Yanbo Mao ; Alexander Gabel ; Thomas Nakel ; Prisca Viehöver ; Thomas Baum ; Dawit G Tekleyohansm ; Dieu Vo ; Ivo Grosse ; Rita Groß-HardtSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaPolyploidization, the increase in genome copies, is considered a major driving force for speciation. We have recently provided the first direct in planta evidence for polyspermy induced polyploidization. Capitalizing on a novel sco1-based polyspermy...
14h
Contributors : Aliza B Rubenstein ; Gregory R Smith ; Ulrika Raue ; Frederique Ruf-Zamojski ; Venugopalan Nair ; Lan Zhou ; Elena Zaslavksy ; Scott Trappe ; Stuart SealfonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSkeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression...
15h
Contributors : Poonam R Pandey ; Amaresh C Panda ; Jen H Yang ; Ji H Noh ; Kyoung M Kim ; Dimitrios Tsitsipatis ; Rachel Munk ; Xiaoling Yang ; Jennifer L Martindale ; Ming W Chang ; Supriyo De ; Kotb Abdelmohsen ; Myriam GorospeSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusBy interacting with proteins and nucleic acids, the vast family of mammalian circRNAs is proposed to influence many biological...
16h
Contributors : Karen E Knudsen ; Jennifer J McCannSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe deubiquitinase USP22 is a member of the SAGA transcriptional activation complex. This study used models of USP22 overexpression and depletion to identify differentially expressed gene networks.
16h
Contributors : Daniel del Valle Morales ; Jackson B Trotman ; Ralf Bundschuh ; Daniel R SchoenbergSeries Type : OtherOrganism : Homo sapiensCap homeostasis is the cyclical process of decapping and recapping that maintains the translation and stability of a subset of the transcriptome. Previous work showed levels of some recapping targets decline following transient expression of an inactive form of RNMT (ΔN-RNMT), likely due to degradation of mRNAs with improperly methylated caps. The current study...
17h
Contributors : Claudia Antunes ; Jorge D Da Silva ; Sonia Guerra-Gomes ; Nuno D Alves ; Fabio Ferreira ; Eduardo Loureiro-Campos ; Miguel R Branco ; Nuno Sousa ; Wolf Reik ; Luisa Pinto ; C Joana MarquesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTET3 is a member of the Ten-eleven translocation (TET) family of enzymes which oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Tet3 is highly expressed in the brain, where 5hmC levels...
19h
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