Contributors : Gunnar H Poplawski ; Riki Kawaguchi ; Giovanni Coppola ; Mark TuszynskiSeries Type : Expression profiling by high throughput sequencingOrganism : In the present study, we identify transcriptional mechanisms associated with corticospinal regeneration. We took advantage of the ability of NPC grafts to support corticospinal regeneration, together with a genetic mouse model (Glt25d2-GFP-L10a mice, in which a bacterial artificial chromosome (BAC) codes for GFP-tagged polyribosomes in...
1h
Contributors : Emam Mehdi ; Mallard Bonnie ; Juan F Medrano ; Angela CanovasSeries Type : Expression profiling by high throughput sequencingOrganism : The proinflammatory response of Monocyte-Derived Macrophages is controlled by host genetics
2h
Contributors : Yajun Tang ; Dong WangSeries Type : Expression profiling by high throughput sequencingOrganism : With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry...
2h
Contributors : Ju-Gyeong Kang ; Ji-Eun Lee ; Kai Ge ; Paul M HwangSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : The physiological effects of the many germline mutations of TP53, encoding the tumor suppressor protein p53, are poorly understood. Here, we report generating a p53 R178C knockin mouse modeling the human TP53 R181C mutation that is notable for its prevalence and prior molecular characterization....
3h
Contributors : Michael A Garland ; Mitra C Geier ; Sean M Bugel ; Cheryl L Dunham ; Joseph M Brown ; Susan C Tilton ; Robyn L TanguaySeries Type : Expression profiling by high throughput sequencingOrganism : Polycyclic aromatic hydrocarbons (PAHs) typically alter gene expression by acting through the aryl hydrocarbon receptor (AHR). In a previous phenotypic screen of over 120 PAHs, we identified four PAHs that induce an ectopic caudal fin (called X-fin) in larval zebrafish: benzo[k]fluoranthene (BkF),...
3h
Contributors : Lauge H Mikkelsen ; Steffen HeegaardSeries Type : Expression profiling by arrayOrganism : NanoString data on 12 conjunctival melanomas and mucosal melanomaThe objective was to compare conjunctival melanoma with other mucosal melanomas at the RNA level using NanoString expression analysis of FFPE material.
3h
GSE143943 Post-sepsis immunosuppression depends on NKT cell regulation of mTOR/IFN-gamma in NK cells
Contributors : Edy Y Kim ; Hadas Ner-Gaon ; Aidan M Cullen ; Jingyu Guo ; Jiyoung Choi ; Tomoyoshi Tamura ; Tal Shay ; Michael B BrennerSeries Type : Expression profiling by high throughput sequencingOrganism : We show a new immunosuppressive function for NKT cells, and the NKT cell-mTOR axis may be a therapeutic target to prevent post-sepsis immunosuppression
3h
Contributors : Kaitlyn Liu ; Gregory Brent ; Jainrong LiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTraumatic Brain Injury (TBI) is associated with disruption of cerebral blood flow leading to localized brain hypoxia. Thyroid hormone (TH) treatment, when administered shortly after injury, has been shown to promote neural protection in rodent TBI models. The mechanism of TH protection, however, is not established. We used mouse primary cortical neurons...
3h
Contributors : Shinji Tanaka ; Hidewaki NakagawaSeries Type : Expression profiling by high throughput sequencingOrganism : Background: The tumor microenvironment can be classified into immunologically active “inflamed” tumors and inactive “non-inflamed” tumors based on the infiltration of cytotoxic immune cells. Previous studies on liver cancer have reported a superior prognosis for inflamed tumors compared to non-inflamed tumors. However, liver cancer is highly heterogeneous immunologically and...
3h
Contributors : Alec R Nickolls ; Michelle M Lee ; David F Espinoza ; Marcin Szczot ; Ruby Lam ; Qi Wang ; Jeanette Beers ; Jizhong Zou ; Minh Q Nguyen ; Hans J Solinski ; Aisha A AlJanahi ; Kory R Johnson ; Michael E Ward ; Alexander T Chesler ; Carsten G BönnemannSeries Type : Expression profiling by high throughput sequencingOrganism : In vitro generation of human peripheral sensory neurons may provide a framework for novel drug screening platforms and disease models of touch and pain. However,...
3h
Contributors : Jun Zhang ; Jie QiSeries Type : Non-coding RNA profiling by arrayOrganism : Using the highly sensitive miRNA array, we screened 220 microRNAs abundant in physiological left ventricular hypertrophy (LVH) and we explored the functions of these miRNAs in the cardiac tissue by Gene Ontology and Kyoto Encyclopedia of Genes annotation. miRNAs showed a high score in the pathway enriched in autophagy. Moreover, the expression levels of miR-26b-5p, miR-204-5p, and miR-497-3p showed an obvious...
3h
Contributors : Chiara Tordonato ; Matteo J Marzi ; Pier P Di Fiore ; Francesco NicassioSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAlthough ectopic overexpression of miRNAs can influence mammary normal and cancer stem cells (SCs/CSCs), their physiological relevance remains uncertain. Here, we found that the miR-146 family is linked to SC identity, since: i) their expression is very high in SCs/CSCs from human/mouse primary mammary tissues; correlates with...
3h
Contributors : Erika Dalmo ; Patrik Johansson ; Maria Niklasson ; Ida Gustavsson ; Sven Nelander ; Bengt WestermarkSeries Type : Expression profiling by high throughput sequencingOrganism : Glioblastoma multiforme (GBM) continues to have a dismal prognosis. Even though detailed information on the genetic aberrations in cell signaling and cell cycle checkpoint control is available, no effective targeted treatment has been developed. Despite the advanced molecular defects, glioblastoma cells...
3h
Contributors : Sandi Chiranjeevi ; Messie Charlie ; Antonio Ramos-Montoya ; Sérgio L Felisbino ; Davies Barry ; Pacey SimonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: RNA sequence analysis identified active proliferation of T cells in the combination therapyMethods: Pten-null tumours were collected 4 hours after the last dose (18th day). Total RNA from tumor samples was isolated using the Allprep kit (Qiagen, Germany). The quantity of the RNA...
3h
Contributors : Qiangsong Tong ; Liduan ZhengSeries Type : Expression profiling by arrayOrganism : Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining public microarray and RNA sequencing datasets, we identified neuroblastoma...
5h
Contributor : Liexiang HuangfuSeries Type : Expression profiling by high throughput sequencingOrganism : Oryza sativaMelatonin plays a potential role in multiple plant developmental processes and stress response. However, there are no reports regarding exogenous melatonin promoting rice seed germination under salinity and nor about the underlying molecular mechanisms at genome-wide. Here, we revealed that exogenous application of melatonin conferred roles in promoting rice seed germination under...
6h
Contributor : Christopher K GlassSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey the lung. Each cell type plays distinct functional roles under homeostatic and inflammatory conditions, but mechanisms establishing their molecular identities and functional potential remain poorly understood....
8h
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
8h
Contributors : Eniko Sajti ; Verena M Link ; Zhengyu Ouyang ; Nathanael J Spann ; Emma Westin ; Casey E Romanoski ; Gregory J Fonseca ; Lawrence S Prince ; Christopher K GlassSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey the lung. Each cell type plays distinct functional roles under homeostatic and inflammatory conditions, but mechanisms establishing...
8h
Contributors : Eniko Sajti ; Verena M Link ; Zhengyu Ouyang ; Nathanael J Spann ; Emma Westin ; Casey E Romanoski ; Gregory J Fonseca ; Lawrence S Prince ; Christopher K GlassSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey the lung. Each cell type plays distinct functional roles under homeostatic and inflammatory conditions, but mechanisms establishing...
8h
Contributor : Gottfrid SjödahlSeries Type : Expression profiling by arrayOrganism : Homo sapiensIt is unclear how urothelial carcinoma of the urinary bladder change, genetically and phenotypically, as patients progress from recurrent non muscle-invasive (NMI) to muscle-invasive (MI) disease or disease that require radical cystectomy. This data set contains gene expression data from 200 samples in a longitudinal study of such patients. Overlap with previously GEO-published cohorts from our lab is...
10h
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Danio rerioThis SuperSeries is composed of the SubSeries listed below.
11h
Contributors : Hyung Joo Lee ; Ting Wang ; Stephen L JohnsonSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioBackground: Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage....
11h
Contributors : Hyung Joo Lee ; Ting Wang ; Stephen L JohnsonSeries Type : Methylation profiling by high throughput sequencingOrganism : Danio rerioBackground: Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage....
11h
Contributors : Hyung Joo Lee ; Ting Wang ; Stephen L JohnsonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Danio rerioBackground: Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration...
11h
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
12h
Contributors : Martin A White ; Elise Darmon ; Manuel A Lopez-Vernaza ; David LeachSeries Type : OtherOrganism : Escherichia coli K-12The effect of a site-specific DNA double-strand break on the abundance of E. coli chromosomal DNA during exponential growth was investigated by marker frequency analysis (MFA).
15h
Contributors : Leon N Schulte ; Marco Metzger ; Jörg VogelSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344Here, we introduce an intestinal tissue model to study human enteric infections. Our model comprises epithelial and endothelial layers, a primary intestinal collagen scaffold, and immune cells. We use Dual RNA-seq to chart the communication amongst several different cell types at the...
16h
Series Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusIntercellular communication orchestrates effective immune responses against disease-causing agents. Extracellular vesicles (EVs) are potent mediators of cell-cell communication. EVs carry bioactive molecules, including microRNAs, which modulate gene expression and function in the recipient cell. Here, we show that formation of cognate primary T-B lymphocyte immune contacts promotes transfer to the B cell of...
18h
Contributors : L Fernandez-Messina ; A Rodríguez-Galán ; V G García de Yébenes ; C Gutiérrez-Vázquez ; S Tenreiro ; A R Ramiro ; F Sanchez-MadridSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusT cell blasts were obtained from wild-type C57BL/6 mice. Six-day culture blast supernatants were ultracentrifuged for small EV obtention and small EV pellet obtained after from 100,000g ultracentrifugation and T cell blasts RNA were isolated for small RNA sequencing;...
18h
Contributors : L Fernandez-Messina ; A Rodríguez-Galán ; V G García de Yébenes ; C Gutiérrez-Vázquez ; S Tenreiro ; A R Ramiro ; F Sanchez-MadridSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusIntercellular communication orchestrates effective immune responses against disease-causing agents. Extracellular vesicles (EVs) are potent mediators of cell-cell communication. EVs carry bioactive molecules, including microRNAs, which modulate gene expression...
18h
Contributors : Takuya Nakagawa ; Masaki Fukuyo ; Atsushi KanedaSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensDNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.
23h
Series Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
23h
Contributors : Takuya Nakagawa ; Masaki Fukuyo ; Atsushi KanedaSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensDNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium MethylationEPIC BeadChip Kit was used to obtain DNA methylation profiles across more than 850,000 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.
23h
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