Contributors : Yongwang Zhang ; Xinyi LuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTelomeres, which locate at the end of chromosomes protect chromosomes from fusion and deterioration. This is essential for cells to maintain genome staibility. We applied RNA-seq, to identify the impact of Terc knockout on the expression of retrotransposons in embryonic stem cells.
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Contributors : Cora Ricker ; Noah Berlow ; Charles KellerSeries Type : Expression profiling by high throughput sequencingOrganism : Canis lupus familiaris ; Mus musculusHere, we report using RNA sequencing isolated from frozen tumor samples from genetically-engineered mouse models and canine samples, as well as a preserved mouse cell culture to determine endotypes, or subtypes with distinct pathobiological mechanisms, of embryonal rhabdomyosarcoma (ERMS) and nonrhabdomyosarcoma soft tissue sarcomas...
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Contributors : Paul Savage ; Alain Pacis ; Hellen Kuasne ; Leah Liu ; Daniel Lai ; Adrian Wan ; Valentina Muñoz-Ramos ; Virginie Pilon ; Anie Monast ; Hong Zhao ; Margarita Souleimanova ; Matthew G Dankner ; Matthew Annis ; Adriana Aguilar-Mahecha ; Nicholas R Bertos ; Jamil Asselah ; Nathaniel Bouganim ; Kevin Petrecca ; Peter M Siegel ; Atilla Omeroglu ; Sohrab P Shah ; Samuel Aparicio ; Mark Basik ; Sarkis Meterissian ; Morag ParkSeries Type : Expression profiling by high...
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Contributors : Lisa Liang ; Ludivine Coudière Morrison ; Nazanin Tatari ; Margaret Stromecki ; Agnes Fresnoza ; Christopher J Porter ; Marc Del Bigio ; Cynthia Hawkins ; Jennifer Chan ; Michael D Taylor ; Vijay Ramaswamy ; Tamra Werbowetski-OgilvieSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe extensive heterogeneity both between and within the medulloblastoma (MB) subgroups underscores a critical need for variant-specific biomarkers and therapeutic...
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Contributors : Benyu Liu ; Zusen FanSeries Type : Expression profiling by arrayOrganism : Mus musculusInvestigation of differentially expressed genes in circKcnt2-deficient ILC3s
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Contributors : Laura R Goodwin ; Matías Alvarez-Saavedra ; Stephen Rennick ; David J PickettsSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusSnf2l and the closely related protein, Snf2h, play a critical role in embryonic and post-natal brain development. Murine models lacking functional Snf2h or Snf2l point to complementary activities of these remodelers; Snf2h cKO mice present with a significantly reduced cerebellum, while Snf2l Ex6DEL cerebella...
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Contributor : Martin L BaschSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed RNAseq on FACS-sorted cells of the lateral wall of the cochlea from neonatal mice. The goal was to identify singaling pathways acting during the differentiation of neural crest progenitors into intermediate cells of the stria.
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Contributors : Yuwen Li ; Fenglin Wang ; Samir El-DahrSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptional profiling of whole kidneys from Six2CreEGFP mice without (WT) or with (KO) homozygously floxed DOT1 alleles at the age of embryonic day 16.5. This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of DOT1 gene in the nephron progenitor population (Six2 positive) and successive changes to the series of events...
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Contributor : Hanlee JiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe report the integrative analysis of single cell genome and transcriptome characteristics of gastric cancer cell lines
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Contributors : Jan U Lohmann ; Andrej MiotkSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Arabidopsis thalianaDuring development and growth, dynamic signals need to be translated into spatially precise and temporally stable gene expression states, which define cell fate. In the context of the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers organ initiation. At the same time, stem cells are continuously...
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Contributor : Guoting LiangSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Solanum lycopersicumIn this study, we identifyed the LncRNAs expressed in S. lycopersicum leaves under different para-hydroxybenzoic acid concentration treatments.
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Contributors : Analilia A Becerra ; Josefat Gregorio Jorge ; Miguel A LopezSeries Type : Expression profiling by high throughput sequencingOrganism : Phaseolus vulgarisCommon bean (Phaseolus vulgaris L.) is an important crop cultivated around the world, mainly in areas susceptible to drought. Since drought is the major environmental factor limiting worldwide crop productivity, efforts have been invested to improve drought resistance in commercial common bean varieties. However, no molecular data...
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GSE142722 CRISPR/Cas9-mediated gene correction in newborn rabbits with hereditary tyrosinemia type I
Series Type : Genome variation profiling by high throughput sequencingOrganism : Oryctolagus cuniculusThis SuperSeries is composed of the SubSeries listed below.
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Contributors : Daniel Fisher ; Nikolaos ParisisSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe identified a species of histone H3 phosphorylated on serine 57 and showed that it is involved in responses to DNA replication stress. Here we asked whether it is specifically localised in the human genome by ChIP-seq from human osteosarcoma cells (U2OS) growing exponentially or treated with 2mM hydroxyurea for 2 hours to stall DNA replication forks
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Contributors : Nan Li ; Shixue Gou ; Jiaowei Wang ; Quanjun Zhang ; Jingke Xie ; Li Li ; Qin Jin ; Ouyang Zhen ; Fangbing Chen ; Weikai Ge ; Hui Shi ; Yanhui Liang ; Huang Xingyun ; Zhenpeng Zhuang ; Xiaozhu Zhao ; Meng Lian ; Yinghua Ye ; Longquan Quan ; Han Wu ; Kepin Wang ; Liangxue LaiSeries Type : Genome variation profiling by high throughput sequencingOrganism : Oryctolagus cuniculusMutations in the metabolic enzyme fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia...
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Contributors : Yu Liu ; Jinghui ZhangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensChIP-seq experiment was carried out to characterize enhancers in one T-ALL PDX sample.
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Contributors : Pan Wang ; Sheng Gong ; Lu Zhao ; Nan WUSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensHIF1α promotes glioblastoma cell proliferation and tumorigenesis under hypoxia conditions, leading to poor prognosis; however, none of the targeted therapies of HIF1α for glioblastoma is success nowadays. Therefore, we focused to look for the reason and wondered whether HIF2α contributed GBM growth. We did gene-chip and found that HIF2α contributed...
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Contributors : Elias O Aniello Federico ; Jochen UtikalSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe aim of this work is to establish the impact of SETDB1 expression in melanoma. SETDB1 was overexpressed in melanoma cell lines (SETDB1 OE) and whole-genome expression profiles were compared to the control ( melanoma cells carrying an empty vector).
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Contributors : Hong-qiang Chen ; Wen-Bin LiuSeries Type : Expression profiling by arrayOrganism : Homo sapiens3-methylcholanthrene (3-MCA) is a typical representative PAH. It has strong toxicity and is an environmental chemical carcinogen. However, the epigenetic mechanisms underlying 3-MCA-induced tumourigenesis are largely unknown.In this study, a model of the 3-MCA-induced malignant transformation of human bronchial epithelial (HBE) cells was established successfully. The profiles of gene expression...
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Contributors : P B Chen ; M R GhadiriSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe gut microbiome is a dynamic, malleable microbial community that can provoke phenotypic changes in the host that promote or suppress the development of disease. In humans and animals, imbalances in the gut microbiome have been associated with numerous ailments ranging from metabolic disorders such as atherosclerosis to neurological disorders such as autism. Yet, despite considerable...
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Contributors : Shi Zhen ; Lim Cindy ; Tran Vuong ; Cui Kairong ; Zhao Keji ; Chen XinSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterTo elucidate endogenous gene expression profiles in germ cells at discrete but continuous differentiation stages, we developed a new experimental strategy that we named Transcriptome Analysis using Single Germline Cyst (TASC).
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Contributors : Xuetao cao ; Qian ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo investigate cell-specific transcriptomes, we clustered the dynamic patterns of mRNAs. A large proportion of genes had significant expression variations among monocytes, imDCs and mDCs. Genes with the same expression levels in either two of the three cell types rarely appeared, which implied heterogeneity of these cells. During DC differentiation and maturation, there were...
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Contributor : N I LimanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe goals of this study are to compare the clusters and pathways of differential genes in scramble microPEP(Scr) and microPEP155(P155) treated THP1-derived dendritic cells.Methods: THP1-derived DCs were treated with P155 or Scr for 2 h and then treated with R848 (1 µg/ml) for another 2 h. All samples were washed twice with PBS, and total RNA was extracted with RNAiso Plus (Takara Bio) and...
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Contributors : Stefano Berto ; Noriyoshi Usui ; Kazuya Toriumi ; Connor Douglas ; Genevieve KonopkaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Macaca mulatta ; Pan troglodytesRecent discussions of human brain evolution have largely focused on increased neuron numbers and changes in their connectivity and expression. However, it is increasingly appreciated that oligodendrocytes play important roles in cognitive function and disease. Whether both...
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Contributor : N I LimanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goals of this study are to analyze the DEGs of the spinal cord cells in scramble microPEP(Scr) or microPEP155(P155) treated EAE mouse model.Methods: mononuclear cells of the spinal cord were isolated using Percol™ gradient centrifugation, washed twice with PBS, and total RNA was extracted with RNAiso Plus (Takara Bio) and purified with magnetic oligo (dT) beads after denaturation. Purified...
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Contributors : Einari A Niskanen ; Joanna K Lempiäinen ; Marjo Malinen ; Jorma J PalvimoSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo analyze the role of BCOR (BCL6 corepressor) in androgen signaling, we used ChIP-seq to analyze chromatin binding of BCOR in androgen and vehicle treated VCaP cells. The role of BCOR in transcription regulation was analyzed from BCOR depleted (siBCOR) and...
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Contributors : Nan Li ; Shixue Gou ; Jiaowei Wang ; Quanjun Zhang ; Jingke Xie ; Li Li ; Qin Jin ; Ouyang Zhen ; Fangbing Chen ; Weikai Ge ; Hui Shi ; Yanhui Liang ; Huang Xingyun ; Zhenpeng Zhuang ; Xiaozhu Zhao ; Meng Lian ; Yinghua Ye ; Longquan Quan ; Han Wu ; Kepin Wang ; Liangxue LaiSeries Type : Genome variation profiling by high throughput sequencingOrganism : Oryctolagus cuniculusMutations in the metabolic enzyme fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia...
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Contributors : Tianqi Wang ; Dong ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMethod: To better understand the mechanism of perforin in regulating liver CD8 T cell-mediated inflammation during NASH, we sorted CD8 T cells from the livers of WT or Prf1null mice fed the MCD diet for 4 weeks and performed mRNA sequencing of these hepatic CD8 T cells. Total RNA was isolated from FACS-separated hepatic CD8 T cells. Transcriptome sequencing libraries were...
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Contributors : Robin Allshire ; Puneet Singh ; Manu Shukla ; Marcel Lafos ; Pin TongSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Schizosaccharomyces pombeHigh coincidence was observed for Hap2 and Arp5 peaks
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Contributors : Joanne M Lind ; Christine L Chiu ; Nerissa L HearnSeries Type : Methylation profiling by arrayOrganism : Homo sapiensGenome wide DNA methylation profiling in saliva samples from individuals with and without coeliac disease. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. The study investigated DNA methylation profiles associated with CD.
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Contributors : Jun P Hong ; Glennys Reynoso ; Prabhakar S Andhey ; Amanda Swain ; Jackson Turner ; Adrianus C Boon ; Florian Krammer ; Ali Ellebedy ; Fabio Zanini ; Maxim Artyomov ; Heather D Hickman ; Michael S DiamondSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCD137 is a costimulatory receptor expressed on natural killer cells, T cells, and subsets of dendritic cells. An agonistic monoclonal antibody (mAb) against CD137 has been used to reduce tumor...
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Contributors : Taylor Morriseau ; Prasoon Agarwal ; Mario Fonseca ; Vern DolinskySeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusGestational diabetes mellitus (GDM) exposure and obesity are strong risk factors for type 2 diabetes development; however, the connections between GDM exposure, postnatal diet and islet dysfunction in offspring metabolic health remain unclear. Reduced glucose-stimulated insulin secretion was observed in islets isolated from...
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Contributors : Jun P Hong ; Glennys Reynoso ; Prabhakar S Andhey ; Amanda Swain ; Jackson Turner ; Adrianus C Boon ; Florian Krammer ; Ali Ellebedy ; Fabio Zanini ; Maxim Artyomov ; Heather D Hickman ; Michael S DiamondSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCD137 is a costimulatory receptor expressed on natural killer cells, T cells, and subsets of dendritic cells. An agonistic monoclonal antibody (mAb) against CD137 has been used to reduce tumor...
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Contributors : Yun Zheng ; Ye Yang ; Dahui LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Panax notoginsengNitrogen is one of the essential elements for plant growth. NH4+ and NO3- are two major forms of absorbing element N for higher plants. In this study we found that the growth of Panax notoginseng is inhibited when only adding ammonium nitrogen fertilizer, and adding nitrate fertilizer can alleviate the toxicity caused by ammonium. We use RNA-seq to identify...
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Series Type : Expression profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
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GSE109910 Difference of gene expression between colorectal tumor tissues with and without metastasis
Contributors : Shuang Wang ; Yiqing WangSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensTo identify the difference of genes expression bewteen colorectal tumor tissues with and without metastasis
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Contributors : Kinya Yokoyama ; Humiaki KanamoriSeries Type : Expression profiling by arrayOrganism : Homo sapiensDuring superficial temporal artery (STA)-middle cerebral artery (MCA) anastomoses, micro-samples of both MCA and STA from the patients with MMD (n=4) and internal carotid artery aneurysm (IA) (n=4) were collected. Using microarray technique, transcriptome-wide analyses were performed. Comparing MCA gene expression profile between MMD and IA, we detected 39 up-regulated and 12 down-regulated...
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GSE108485 Gene expression analysis of the hippocampus in Il18+/+ and Il18-/- mice at 12 weeks of age
Contributors : Kyosuke Yamanishi ; Hisato MatsunagaSeries Type : Expression profiling by arrayOrganism : Mus musculusInterleukin-18 (IL-18) was one of the inflammatory cytokines and related to major depressive disorder (MDD) and dementia. Compared with Il18+/+ mice, IL-18 knockout (Il18−/−) mice developed impaired learning and memory, more anxiety, and less motivation. To reveal the mechanism, the microarray was performed.
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Contributors : Kinya Yokoyama ; Humiaki KanamoriSeries Type : Expression profiling by arrayOrganism : Homo sapiensDuring superficial temporal artery (STA)-middle cerebral artery (MCA) anastomoses, micro-samples of both MCA and STA from the patients with MMD (n=4) and internal carotid artery aneurysm (IA) (n=4) were collected. Using microarray technique, transcriptome-wide analyses were performed. Comparing MCA gene expression profile between MMD and IA, we detected 39 up-regulated and 12 down-regulated...
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Contributors : Catharina Melzer ; Ralf HassSeries Type : Expression profiling by arrayOrganism : Homo sapiensCo-cultures of MSC with neoplastic MCF10A cells demonstrated hybrid cell formation between 0.3% and about 2% of the populations within 72h
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Contributors : Chao Zhou ; Dechun ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Sorghum bicolorThe applications of plant callus regeneration has been widely spreaded in agricultural improvement. By using immature sorghum embryos as explants, progress in successful genetic transformation has been made in sorghum. However, the underlying mechanism of callus differentiation is still largely unknown in sorghum. Here, we described three types of callus with different...
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Contributors : Lin Hsien-Yi ; Yang Liang-TungSeries Type : Expression profiling by arrayOrganism : Mus musculusHes1 regulates hair follicle regenerative cyclingWe used microarrays to profile the global gene expression of hair follicle stem cells in the telogen phase at P70 after depilation at P49. These microarray analysis were designed to identify the signaling networks regualting hair follicle stem cell behavior in the presence or absence of Hes1.
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Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
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Contributors : Juan Madoz-Gúrpide ; Federico Rojo ; Sandra Zazo ; Paula González-AlonsoSeries Type : Expression profiling by arrayOrganism : Homo sapiensBackground: The addition of the anti-HER2 antibody pertuzumab to trastuzumab/chemotherapy treatment in HER2+ breast cancer significantly improves clinical outcome. Concomitantly, the drug-antibody conjugate T-DM1 (trastuzumab-emantasine) has demonstrated efficacy, at least equal, to the combination of trastuzumab/chemotherapy. Scientific, economic...
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Contributors : Yingyue Zhou ; Wilbur M Song ; Prabhakar S Andhey ; Amanda Swain ; Tyler Levy ; Kelly R Miller ; Pietro L Poliani ; Manuela Cominelli ; Shikha Grover ; Susan Gilfillan ; Marina Cella ; Tyler K Ulland ; Konstantin Zaitsev ; Akinori Miyashita ; Takeshi Ikeuchi ; Makoto Sainouchi ; Akiyoshi Kakita ; David A Bennett ; Julie A Schneider ; Michael R Nichols ; Sean A Beausoleil ; Jason Ulrich ; David M Holtzman ; Maxim M Artyomov ; Marco ColonnaSeries Type : Expression profiling...
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Contributors : Cedric Mombereau ; Tanay Ghosh ; Matthias GroszerSeries Type : Expression profiling by arrayOrganism : Mus musculusFoxp2 heterozygous mice and wildtype mice were injected with cocaine or saline, 1h post-injection nucleus acumbens RNA was extracted and analysedWe have tested a potential role for the transcription factor Foxp2 in dopamine signaling and reward associated synaptic plasticity and behavior. We found that Foxp2 is acutely downregulated in reward associated circuits in...
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Contributors : Jun Cho ; Diane Mathis ; Christophe BenoistSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusFoxp3+CD4+ regulatory T cells (Tregs) play important roles in controlling both homeostatic processes and immune responses at the tissue and organismal levels. For example, Tregs promote muscle regeneration in acute or chronic injury models by direct effects on local muscle progenitor cells as well as on infiltrating inflammatory cells. Muscle Tregs have...
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Contributor : Claude AsselinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBoth HDAC1 and HDAC2 are epigenetic erasers that drive specific and redundant gene expression patterns, in part by removing acetyl groups on histones. Deletion of these Hdac in intestinal epithelial cell (IEC) in vivo alters intestinal homeostasis, dependent on the Hdac deleted and the level of expression of both. To determine the intrinsic specific IEC function of HDAC1 and HDAC2,...
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Contributors : Yingyue Zhou ; Wilbur M Song ; Prabhakar S Andhey ; Amanda Swain ; Tyler Levy ; Kelly R Miller ; Pietro L Poliani ; Manuela Cominelli ; Shikha Grover ; Susan Gilfillan ; Marina Cella ; Tyler K Ulland ; Konstantin Zaitsev ; Akinori Miyashita ; Takeshi Ikeuchi ; Makoto Sainouchi ; Akiyoshi Kakita ; David A Bennett ; Julie A Schneider ; Michael R Nichols ; Sean A Beausoleil ; Jason Ulrich ; David M Holtzman ; Maxim M Artyomov ; Marco ColonnaSeries Type : Expression profiling...
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Contributors : Ying Ding ; Jinho KimSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThrough multi-dimensional characterization of longitudinally paired breast cancers during NAC treatment, we have identified dynamic changes in the tumor cellular and molecular states and derived insights into the mechanism of action as well as resistance to an important class of therapy.
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Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
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Contributors : Julian Carretero ; Takeshi ShimamuraSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe have employed a transcriptomic approach to find a molecular target that could compensate for the loss of EGFR signaling in NSCLC cell lines with acquired resistance to EGFR TKIs with an EMT phenotype.
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Contributor : Feizhen WuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDNA methylation at the 5-position of cytosine (5mC) is a crucial epigenetic mark in regulating biological processes including gene silencing, gene imprinting, and X chromosome inactivation. It has long been questioned how de novo DNA 5mC patterns are established in different genomic regions and whether histone modifications crosstalk to the process. Here, we report a previously uncovered...
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Contributors : Natalia Kosyakova ; Derek D Kao ; Francesc López-Giráldez ; Susann Spindler ; Morven Graham ; Kevin J James ; Jee W Shin ; Xinran Liu ; Gregory T Tietjen ; Jordan S Pober ; William G ChangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAims: Formation of a perfusable microvascular network (μVN) is critical for tissue engineering of solid organs. Stromal cells can support endothelial cell (EC) self-assembly into a μVN, but distinct stromal...
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Contributor : Feizhen WuSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensDNA methylation at the 5-position of cytosine (5mC) is a crucial epigenetic mark in regulating biological processes including gene silencing, gene imprinting, and X chromosome inactivation. It has long been questioned how de novo DNA 5mC patterns are established in different genomic regions and whether histone modifications crosstalk to the process. Here, we report a previously uncovered...
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Contributors : Rebecca Treger ; Akiko Iwasaki ; Scott Pope ; Yong Kong ; Maria Tokuyama ; Manabu TauraSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTranscriptional silencing of endogenous retroviruses (ERV) defends against active retrotransposition and disease, including overproduction of non-ecotropic ERV (NEERV) envelope and resultant nephritis observed in lupus-prone mice. However,...
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Contributor : Feizhen WuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensDNA methylation at the 5-position of cytosine (5mC) is a crucial epigenetic mark in regulating biological processes including gene silencing, gene imprinting, and X chromosome inactivation. It has long been questioned how de novo DNA 5mC patterns are established in different genomic regions and whether histone modifications crosstalk to the process. Here, we report a previously...
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Contributors : Liu Xingguang ; Zhou QingqingSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: The purpose of this study is to detect activated or silenced genes during Kdm2b-deficient peritoneal macrophages and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis.Methods: Mouse peritoneal macrophages were harvested from mice 4 days after thioglycollate (BD, Sparks, MD) injection....
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Contributors : Nicole A Walter ; Robert HitzemannSeries Type : Expression profiling by high throughput sequencingOrganism : Macaca fascicularisThe data presented here are the first to use a longitudinal biopsy strategy to examine how chronic ethanol consumption affects gene expression in the primate PFC.
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Contributor : Attila TothSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA from female gonads (C57/BL6xDBA/2 background) at different developmental stages (11.5dpc, 12.5dpc, 14.5dpc, 16.5dpc, 18.5dpc, 20.5dpc – dpc: days post coitum) together with RNA from adult testes and 17 different somatic tissues was used for transcriptome comparison.
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Contributors : Roberta Brinton ; Shang Yuan ; Mishra Aarti ; Wang Tian ; Wang Yiwei ; Desai Maunil ; Chen Shuhua ; Mao ZisuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusLate onset Alzheimer’s disease (LOAD) is a progressive neurodegenerative disease with four well-established risk factors: age, APOE4 genotype, female chromosomal sex, and maternal history of AD. Each risk factor impacts multiple systems, making LOAD a complex systems biology challenge....
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Contributors : Jung W Eun ; Sang Y Kim ; Suk W NamSeries Type : Expression profiling by arrayOrganism : Homo sapienswe examined 24 pericardial effusion patients and obtained pericardial fluid. To identify novel biomarker for detection cancer, detected transcriptome-based molecualr signature of compare pathologic cancer patients and non-cancer patients.
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Contributors : Yordanis Perez-Llano ; Maria d Sanchez-CarbenteSeries Type : Expression profiling by high throughput sequencingOrganism : Aspergillus sydowiiThe mechanisms of cellular and molecular adaptation of fungi to salinity have been commonly drawn from halotolerant strains, although some exceptions in basidiomycete fungi can be found. These studies have been conducted in settings where cells are subjected to stress, either hypo or hyperosmotic, which can be a confounding factor in describing...
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Contributor : Ryosuke MuroyamaSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiens ; Mus musculus ; Rattus norvegicusTo comprehensively characterize the biological function of fusion HBx, the expression level of miRNAs in mock and fusiion HBx-knockdowned cells was investigated based on microarray.
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Contributors : Alec R Nickolls ; Carsten G BönnemannSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn vitro generation of human peripheral sensory neurons may provide a framework for novel drug screening platforms and disease models of touch and pain. However, derivation of a functionally pure sensory neuron population remains a major unmet challenge. We discovered that, by expressing the transcription factors NGN2 and BRN3A, human pluripotent stem cells can...
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Contributors : Lixin Rui ; Li Lu ; Fen ZhuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWhole transcriptome profiling in Diffuse large B cell lymphoma (DLBCL) cells with and wothout PRMT5 knockout revealed important pro-survival pathways that are regulated by PRMT5.
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Contributors : Andrew Ransick ; Albert D Kim ; Guilherme De Sena Brandine ; Nils O Lindstrom ; Andrew McMahonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo characterize the cellular diversity in the human kidney cortical nephrogenic niche we dissociated cells from the cortex and performed 10X Genomics single-cell RNA sequencing.
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Contributors : Jie Chen ; Qimin ZhanSeries Type : Expression profiling by arrayOrganism : Homo sapiensKYSE410 cells were tranfected with NOX5 plasmid in the presence or absence of HIF-1α inhibitor-BAY87-2243 and mRNA expression of tumor-promoting molecules were assayed by RiboArray Human mRNA Arrayinvestigation of the critical gene participating in the process of NOX5/HIF-1α-mediated ESCC progression.
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Series Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
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Contributors : Li Wenyang ; Wei YongSeries Type : Expression profiling by arrayOrganism : Homo sapiensIn the lung metastatic breast cancer MDA-MB231 subline LM2 cells, knockdown of USP20 results in similar changes of a list of migration/invasion-related genes as knockdown of SLUG, and SLUG protein is identified as a target of USP20 for deubiquitination.
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Contributors : Veronique Azuara ; Ed Curry ; Wout MegchelenbrinkSeries Type : OtherOrganism : Mus musculusWe uncover a pivotal role for ESRRB in demarcating ESC-specific enhancer units, and propose that ESRRB’s developmentally-regulated extinction precipitates their decommissioning with impact on the rewiring of the pluripotency transcriptional programme upon embryo implantation.
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Series Type : Non-coding RNA profiling by high throughput sequencingOrganism : Rosa rugosaThis SuperSeries is composed of the SubSeries listed below.
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Contributors : Sebastian Scheer ; Adele BurghareSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusChIP sequencing of naïve Th, bona fide Th1 and bona fide Th2 cells
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Contributor : Ryoji YaoSeries Type : Expression profiling by arrayOrganism : Homo sapiensFAP is an autosomal-dominant inherited disease caused by germline mutations in the APC gene 1. Two major FAP phenotypes, CFAP and AFAP, can be distinguished based on polyp numbers and age of onset. CFAP is characterized by the presence of hundreds to thousands of polyps. About half of these patients develop adenomas by age 15, and 95% develop adenomas by age 35. AFAP patients exhibit a milder phenotype than...
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Contributors : Huang Shisheng ; Ren Chao ; Yuan Jie ; Qiao Yunbo ; Liu Zhen ; Shu WenjieSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe used an combination of long-read and short-read sequencing data to explore the transcriptome of preimplantation embryo
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Contributors : Carmen J Narvaez ; Samantha K Mall ; Aaron Fountain ; Brian A Parr ; Sridar V Chittur ; Boris I Kokorin ; Stephen F Botsford ; Joseph F StartariSeries Type : Expression profiling by arrayOrganism : Homo sapiensA novel application of a non-invasive, electromagnetic field technology has a significant inhibitory effect on the proliferation of glioblastoma multiforme U-87 MG cells in culture. This study reports the cellular and molecular responses of U-87 MG cells to the effects of a...
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Contributor : Jari KoistinahoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMutations in presenilin 1 (PSEN1) cause a familiar form of Alzheimer's disease (AD). We have obtained skin biopsies from two individuals carrying PSEN1 exon9 deletion and reprogrammed skin fibroblasts into induced pluripotent stem cells (iPSCs). To get controls, we have corrected PSEN1 exon9 deletion by CRISPR/Cas9 technique. Since astrocytes play role in AD pathogenesis, we further...
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Contributor : Yuewen TangSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusNeural stem cells (NSCs) are valuable for both basic research and clinical application. We previously reported a chemical cocktail that could reprogram somatic cells into neural progenitor cells. However, the process of chemical induction is complex and the underlying mechanism remains largely elusive. Here, we identified...
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Contributors : Lawrence T Reiter ; Kevin A HopeSeries Type : Expression profiling by arrayOrganism : Drosophila melanogasterIn order to identify common gene expression across other gliopathic bang senstiive genes (i.e. genes that when knocked down or over expressed by repo-GAL4 cause seizures) we crossed six UAS-RNAi or UAS-over-expression lines for known bang senstive genes to repo-GAL4. We pooled total RNA from brains of these animals in equal amounts and ran microarray analysis to search for...
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Contributors : Tamara Fernandez-Calero ; Charly Jehanno ; Denis Habauzit ; Stephane Avener ; Frederic Percevault ; Noureddine Boujrad ; Pascale Le Goff ; Monica Marin ; Denis Michel ; Raphaël Métivier ; Gilles FlouriotSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensEstrogen receptor (ERα) is central in driving the development of hormone-dependent breast cancers. A major challenge in treating these cancers is to understand and struggle...
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Contributors : Lawrence T Reiter ; Kevin A HopeSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterFly Dube3a was expressed using either the neuronal driver (elav-GAL4) or the glial driver (Repo-GAL4). RNAseq data was compared among groups (elav>Dube3a), (repo>Dube3a) and (Dube3a alone). Expression was measured in whole dissected fly brain.
2h
Contributors : Guangyong Sun ; Dong ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMethods: To better understand the role of OX40 in the regulation of monocyte activation and polarization, OX40/Fc- or control IgG-treated liver monocytes were compared in a transcriptome sequencing study. Total RNA was isolated from FACS-separated hepatic monocytes. Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®...
2h
Contributors : Jessica L Flesher ; Rolando Ruiz ; Anand K GanesanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMITF, a gene that is mutated in familial melanoma and Waardenburg syndrome, encodes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini. It is not completely understood how these isoforms influence pigmentation in different tissues and how expression of these independent isoforms of...
2h
Contributors : Caixia Liu ; Shukai Zheng ; Meijie YeSeries Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensTo invstigate lncRNA expression in long-term cigarette smoking in immortal esophageal cell SHEE, we have employed the microarray lncRNA expression profile as a platform to identify cigaretted-related oncogenes and cancer surpressors.
2h
Contributor : Xin DengSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Pseudomonas savastanoi pv. phaseolicola 1448APseudomonas syringae, a Gram-negative plant pathogen, infects more than 50 crops with its type III secretion system (T3SS) and causes severe economic losses around the world. Although the mechanisms of virulence-associated regulators of P. syringae T3SS have been studied for decades, the crosstalk...
2h
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Other ; Methylation profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
2h
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Alen Faiz ; Maarten van den BergeSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiens ; synthetic constructTo investigate whether expression of microRNAs (miRNAs) are modulated by ICS treatment and whether this change in microRNA expression relates to improved clinical outcomes in COPD patients.
2h
Contributors : Soledad A Camolotto ; Veronika K Belova ; Luke Torre-Healy ; Chris Stubben ; Richard Moffit ; Eric L SnyderSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma is an aggressive disease with a dismal five-year survival of 5%. Gene expression profiling has been instrumental for subtype classification in cancer, highlighting fundamental differences in tumors at the molecular level. Over the last years, multiple genomics...
2h
Contributors : Stephen M Beverley ; Britta A AndersonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Leishmania majorWe sought to identify nuclease-hypersensitive sites and to quantify nucleosome positions in an effort to identify cis-regulatory elements in the protozoan parasite Leishmania major. Using micrococcal nuclease digestion of chromatin (MNAse-seq), we report that few nuclease hypersensitive sites are present within the presumed regions of RNA polymerase...
2h
Contributors : Soledad A Camolotto ; Veronika K Belova ; Luke Torre-Healy ; Hannah Conway ; Chris Stubben ; Richard MoffitSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma is an aggressive disease with a dismal five-year survival of 5%. Gene expression profiling has been instrumental for subtype classification in cancer, highlighting fundamental differences in tumors at the molecular level. Over the last years, multiple genomics...
2h
Contributors : Soledad A Camolotto ; Veronika K Belova ; Luke Torre-Healy ; Chris Stubben ; Richard Moffit ; Eric L SnyderSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma is an aggressive disease with a dismal five-year survival of 5%. Gene expression profiling has been instrumental for subtype classification in cancer, highlighting fundamental differences in tumors at the molecular level. Over the last years, multiple genomics...
2h
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Jacquelyn A Myers ; Laurie A SteinerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusSETD8 is the sole methyltransferase capable of mono-methylating histone H4, lysine 20. SETD8 is highly expressed in erythroid cells and erythroid deletion of Setd8 is embryonic lethal by embryonic day 11.5 (E11.5) due to profound anemia, suggesting it has an erythroid-specific function. To gain insights into the function of SETD8 during erythroid...
2h
Contributors : Ping Lu ; Guang Yang ; Wen He ; Wanwan Wu ; Lingbin Qi ; Shijun Shen ; Guoping Fan ; Zhigang Xue ; Peng Zhang ; Cizhong Jiang ; Peng ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Macaca fascicularis ; Rattus norvegicusNonalcoholic steatohepatitis (NASH) is an aggressive liver disease threatening public health, however its natural history is poorly understood. Unlike ob/ob mice, Lep∆I14/∆I14 rats develop unique NASH phenotype with an inflection...
2h
Contributors : Millissia B Maamar ; Daniel Beck ; Eric Nilsson ; John R McCarrey ; Michael K SkinnerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Rattus norvegicusThis study was designed to investigate the developmental origins of the transgenerational differential histone retention sites (called DHRs) during gametogenesis of the sperm. Vinclozolin and DDT were independently used to promote the epigenetic transgenerational inheritance of these DHRs. Male...
2h
Contributors : Yan Li ; Yang Song ; Mingzhou LiSeries Type : Expression profiling by high throughput sequencingOrganism : Sus scrofaTo optimize the genome annotation, nine tissue and one pool RNA libraries (i.e. heart, liver, spleen, lung, kidney, muscle, fat, ovary, pool.) were constructed using the Illumina mRNA-spleeneq Prep Kit
2h
Contributors : Elena Grossi ; Enrique Goñi ; Maite HuarteSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA is an essential component of the chromatin, influencing genome organization and expression. To investigate the role of lncRNAs in epigenetic activation, we profiled the RNA interactome of SWI/SNF complexes in proliferating and senescent conditions, when cells undergo widespread chromatin rearrangements. The isolation of transcripts associated to SMARCB1...
4h
Contributors : Elena Grossi ; Enrique Goñi ; Maite HuarteSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA is an essential component of the chromatin, influencing genome organization and expression. To investigate the role of lncRNAs in epigenetic activation, we profiled the RNA interactome of SWI/SNF complexes in proliferating and senescent conditions, when cells undergo widespread chromatin rearrangements. The isolation of transcripts associated to SMARCB1...
4h
Contributors : Elena Grossi ; Enrique Goñi ; Maite HuarteSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensRNA is an essential component of the chromatin, influencing genome organization and expression. To investigate the role of lncRNAs in epigenetic activation, we profiled the RNA interactome of SWI/SNF complexes in proliferating and senescent conditions, when cells undergo widespread chromatin rearrangements. The isolation of transcripts associated...
4h
Series Type : Expression profiling by high throughput sequencing ; Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
10h
Contributors : Jinsong Li ; Weiguo ZouSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusFunctional mutagenic screening has been used to identify key factors required for a wide range of developmental processes. However, such screens can only be successfully applied in lower organisms. Here, through combined application of androgenetic haploid embryonic stem cells (haESCs) and CRISPR-Cas9-based genome editing, we quickly identify pivotal factors involved in early...
11h
Contributors : Minerva S Trejo-Arellano ; Saher Mehdi ; Jennifer de Jonge ; Eva Dvorák Tomastíková ; Claudia Köhler ; Hennig LarsSeries Type : Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thalianaSenescence occurs in a programmed manner to dismantle the vegetative tissues and redirect the nutrients towards metabolic pathways supporting reproductive success. External factors can trigger the senescence program as...
11h
Contributors : Paul N Valdmanis ; Meredith M CourseSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusRNA interference (RNAi) is a promising gene therapy strategy for targeting dominant mutations. This therapy leverages small hairpin RNAs (shRNAs) to knock down gene expression; however, delivery of too much shRNA can disrupt the processing of endogenous microRNAs (miRNAs), and lead to toxicity. In this study, we sought to understand the effect that excessive...
16h
Contributors : Fengqi Li ; Katarzyna M Okreglicka ; Lea M Pohlmeier ; Christoph Schneider ; Manfred KopfSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe studied alveolar macrophage (AM) development after single and competitive transplantation of different precursors from YS, fetal liver, and lung into neonatal Csf2ra-/- mice, which lack endogenous AM. Fetal monocytes, promoted by Myb, outcompeted primitive MΦ (pMΦ) in empty AM niches and preferentially...
17h
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