Contributor : Yuliang WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome with no cure. To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via an engineered microRNA maturation cocktail that upregulated the epigenetic regulator, HOPX....
9h
Contributors : Yi Wu ; Keshi Chen ; Xingguo LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMetabolic reprogramming has emerged as key regulators of cell fate decisions. Whereas the glucose and amino acid metabolism have been extensively documented, the roles of lipid metabolism in pluripotency remain largely unexplored. Here, we report that the CDP-Ethanolamine (CDP-Etn) pathway for phosphatidylethanolamine synthesis is required for somatic cell reprogramming...
9h
Contributor : Minh LeSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusRNA was purified from 4T1 and 4TO7 cells and their EVs
9h
Contributors : Yoshiaki Kubota ; Yutaka SuzukiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSingle cell RNA sequencing for mesenteric CD31+ cells derived from control and endothelial-specific Folliculin (Flcn) knockout mice at postnatal day 8
10h
Contributors : Iain R Searle ; Wenbin ZhouSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Arabidopsis thalianaWe show that trm5 plants have less m1G in tRNAs, a slower leaf initiation rate, delayed flowering, and reduced primary root length. Late flowering correlates with reduced transcription of floral activators CO, FT, SOC1 and AP1. We also show that TRM5 methylates tRNA position 37 of several nucleus-encoded...
11h
Contributors : Servando Giraldez ; Steven I ReedSeries Type : Genome variation profiling by SNP array ; Genome variation profiling by genome tiling arrayOrganism : Homo sapiensCyclin E, a key cell cycle regulatory protein, has been linked to oncogenesis when dysregulated. We have previously shown that overexpression of cyclin E causes replication stress, leading to failure to complete replication at specific chromosomal loci during S phase of the cell cycle. This, in turn promotes chromosomal...
1d
Contributors : Claire Bertet ; Bilal El Waly ; Mathilde Paris ; Karine Magalon ; Marie Falque ; Pascale DurbecSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAfter demyelinating insult, the neuronal progenitors of the adult mouse sub-ventricular zone (SVZ) called neuroblasts convert into oligodendrocytes that participate to the remyelination process. We use this rare example of spontaneous fate conversion to identify the molecular mechanisms governing...
1d
Contributors : Jay K Kolls ; Taylor Eddens ; Mingquan Zheng ; William HorneSeries Type : Expression profiling by high throughput sequencingOrganism : Pneumocystis murinaPneumocystis pneumonia is the most common serious opportunistic infection in patients with HIV/AIDS. Furthermore, Pneumocystis pneumonia is a feared complication of the immunosuppressive drug regimens used to treat autoimmunity, malignancy, and post-transplantation rejection. With an increasing at-risk population, there is a strong...
1d
Contributors : Michèle SOUYRI ; Laurence PETITSeries Type : Expression profiling by arrayOrganism : Mus musculusHSC-enriched LSK CD150+CD48- and Lin+ hematopoietic populations were sorted from C57Bl6 adult bone marrow. Their transcriptome was established, and pair-wise comparison performed to establish molecular signatures specific of adult HSCs that could be compared to molecular signatures from AGM, fetal liver or placenta HSCs.
1d
Contributors : Michèle SOUYRI ; Laurence PETITSeries Type : Expression profiling by arrayOrganism : Mus musculusWe sorted endothelial (EC), hematopoietic (HC) and hematopoietic stem/progenitor (HSPC) cell populations from AGM of E11.5 C57Bl6 embryos, established and compared their transcriptome to highlight specific regulators of hematopoietic emergence.
1d
Contributor : Tsuyoshi OsawaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe conditions of the tumor microenvironment, such as nutrient starvation, play critical roles in cancer progression. However, the role of glutamine deprivation in cancer progression is not studied as extensively as that of hypoxia. Here, we show that glutamine starvation triggered down-regulation of PCYT2 by stimulating accumulation of PEtn. Interestingly, glutamine upregulated series...
2d
Contributors : Matthew L Chang ; Sanny Moussette ; Enrique Gamero-Estevez ; Jose H Galvez ; Victoria Chiwara ; Indra R Gupta ; Aimee K Ryan ; Anna K NaumovaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Identifying the biological pathways affected by the deletion of the zona pellucida binding protein 2 in mouse lungs at different time pointsMethod: RNA profiles of wild type C57BL6/J mice and Zpbp2 homozygous knock-out lungs were generated using...
2d
Contributors : Takayuki Katsuyama ; Vaishali R MoultonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: The goals of this study are to determine the role of the serine/ arginine-rich splicing factor 1 (SRSF1) in T cells and autoimmune disease.
2d
Contributor : Hiroyoshi NishikawaSeries Type : Expression profiling by arrayOrganism : Mus musculusWe report the gene expression profiles of FACS-sorted OT-I cells stimulated with N4 or Y3 peptide with or without corticosteroids.
2d
Contributors : Luis Arturo Baiza Gutman ; Araceli Rubí Vietma RodriguezSeries Type : Expression profiling by arrayOrganism : Homo sapiensDiabetes and breast cancer are common diseases with a major impact on the health sector in Mexico and worldwide. Epidemiological and experimental works support the link between type 2 diabetes and breast cancer; these data support that insulin resistance, hyperglycemia, hyperinsulinemia, and elevated levels of IGF-1 in patients with type II diabetes mellitus promote...
2d
Contributors : Isha Sengupta ; Dipanwita Das ; Shivaram P Singh ; Runu Chakravarty ; Chandrima DasSeries Type : Expression profiling by arrayOrganism : Homo sapiensHepatitis B virus (HBV), belonging to Hepadnaviridae family, remains undetected in early infection and is known to be the cause of several hepatic diseases leading to cirrhosis and hepatocellular carcinoma. We have found that PML-Nuclear Body Speckled 110kDa (Sp110), is hyper-expressed upon HBV infection and intriguingly, Sp110 knock-down...
2d
Contributors : Kayla Viets ; Robert J Johnston Jr.Series Type : OtherOrganism : Drosophila melanogasterThe goal of this study was to examine chromosome topology in Drosophila larval eye and antennal discs by identifying topologically associating domains (TADs) across the genome. TADs were compared between the eye and antennal disc to determine whether they contribute to cell-type-specific homologous pairing and transvection.
2d
Contributors : Antwi-Boasiako Oteng ; Philip M Ruppert ; Lily Boutens ; Wieneke Dijk ; Xanthe A van Dierendonck ; Gunilla Olivecrona ; Rinke Stienstra ; Sander KerstenSeries Type : Expression profiling by arrayOrganism : Mus musculusANGPTL4 regulates plasma lipids, making it an attractive target for correcting dyslipidemia. However, ANGPTL4 inactivation in mice fed a high fat diet causes chylous ascites, an acute-phase response, and mesenteric lymphadenopathy. Here, we studied the role of ANGPTL4...
2d
Contributors : Gesa M Richter ; Arne S SchaeferSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHealthy ex vivo biopsies from masticatory mucosa from 17 current and 21 never smokers were analysed using whole transcriptome RNA sequencing (16 mio reads/sample), showing significantly increased expression of CYP1B1 in smokers compared to non-smokers (p = 2.2 × 10−14), together with 13 significantly upregulated transcripts. Six transcripts were significantly downregulated.
2d
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
2d
Contributors : Tomassoni-Ardori Francesco ; Skyler Kuhn ; Vishal Koparde ; Lino TessarolloSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBrain Derived Neurotrophic Factor (BDNF) is a potent modulator of brain synaptic plasticity. Signaling defects caused by dysregulation of its NTrk2 (TrkB) kinase (TrkB.FL) and truncated receptors (TrkB.T1) have been linked to the pathophysiology of several neurological and neurodegenerative disorders. We found that upregulation...
2d
Contributors : Matthew L Chang ; Sanny Moussette ; Enrique Gamero-Estevez ; Jose H Galvez ; Victoria Chiwara ; Indra R Gupta ; Aimee K Ryan ; Anna K NaumovaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Identifying the biological pathways affected by the deletion of the zona pellucida binding protein 2 in mouse lungs at different time pointsMethod: RNA profiles of wild type C57BL6/J mice and Zpbp2 homozygous knock-out lungs were generated using...
2d
Contributors : Qian Zhu ; Nan Liu ; Guo-cheng Yuan ; Stuart OrkinSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe introduce CUT&RUNTools (https://bitbucket.org/qzhudfci/cutruntools/) as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information...
2d
Contributors : Artyom Kiselev ; Alexey Sergushichev ; Alexander Predeus ; Anna KostarevaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEven though genetic studies of individuals with neuromuscular diseases have uncovered the molecular background of many cardiac disorders such as cardiomyopathies and inherited arrhythmic syndromes, the genetic cause of a proportion of cardiomyopathies associated with neuromuscular phenotype still remains unknown. Here,...
2d
Contributors : Patrick A Fletcher ; James IbenSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusUnderstanding of physiology and pathology of an organ composed of variety of cell populations depends critically on genome-wide information on each cell type. Here, we report single-cell transcriptome profiling of over 6800 freshly dispersed anterior pituitary cells from postpubertal male and female rats. Six pituitary-specific cell types were identified based...
2d
Contributors : Celine Pangault ; Thierry Fest ; Fabienne Desmots ; Karin TarteSeries Type : Expression profiling by arrayOrganism : Homo sapiensCD40L and IL-21 are major contributors to the transcriptional emergency of PC identify genes in committed B cells. In order to decipher specific CD40L- and IL21-targeted genes, fresly purified human tonsil centroblasts (n=6) were cultured for 3 hours in presence or not of CD40L and IL-21 before transciptome analysis were performed.
2d
Contributors : Celine Pangault ; Thierry Fest ; Fabienne Desmots ; Karin TarteSeries Type : Expression profiling by arrayOrganism : Homo sapiensGEP on Affymetrix U133+2.0 microarrays was performed on 6 centroblasts and 6 paired centrocytes from human tonsils in order to explore CB/CC transition and GC-B cell specific signatures
2d
Contributors : Ray -Chang Wu ; In-Chi Young ; Yu-Fang Chang ; Sung-Ting Chuang ; Antoun Tougaji ; Mei-Yi WuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPhosphatase and tensin homologue (PTEN) is the most frequently mutated tumor suppressor gene in human prostate cancer. Synthetic essentiality is defined as cancer that harbors a specific tumor suppressor deficiency is dependent on synthetic-essential genes for the malignant phenotypes. Recently, targeting...
2d
Contributors : Ray-Chang Wu ; In-Chi Young ; Yu-Fang Chang ; Sung-Ting Chuang ; Antoun Tougaji ; Mei-Yi WuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensPhosphatase and tensin homologue (PTEN) is the most frequently mutated tumor suppressor gene in human prostate cancer. Synthetic essentiality is defined as cancer that harbors a specific tumor suppressor deficiency is dependent on synthetic-essential genes for the malignant phenotypes. Recently,...
2d
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
2d
Contributors : Mathew Dukinfield ; Eleni Maniati ; Jun Wang ; Kairbaan Hodivala-DilkeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCoronary microvascular dysfunction combined with maladaptive cardiomyocyte morphology and energetics are major contributors towards heart failure advancement. Thus dually enhancing cardiac angiogenesis and targeting cardiomyocyte function to slow, or reverse, the development of heart failure is a logical step towards improved...
2d
Contributors : Nuria Gago-López ; Osvaldo Grana ; Guillermo Martín-Serrano ; Erwin F WagnerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusUsing lineage-tracing in a well-established psoriasis-like mouse model with inducible epidermal deletion of c-Jun and JunB, we found that mutant HF-SCs survive and express a broad group of pro-inflammatory cytokines, whereas mutant inter-follicular epidermal cells (IFE) disappear over time. Mutant HF-SCs initiate epidermal...
3d
Contributors : Renátó Kovács ; Ágnes JakabSeries Type : Expression profiling by high throughput sequencingOrganism : Candida parapsilosisTyrosol plays a key role in fungal morphogenesis and biofilm development. Also, it has a remarkable antifungal effect at supraphysiological concentrations. However, the background of the antifungal effect remains unknown, especially in the case of non-albicans Candida species such as Candida parapsilosis We examined the effect of tyrosol on the growth, adhesion,...
3d
Contributors : Sim W Jing ; Jean P Thiery ; Tan T ZeaSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusAberrant c-Met activation and upregulation of its cognate ligand HGF are frequently observed in bladder cancer and have been shown to regulate downstream pathways involved in proliferation, motility, and invasion. The precise mechanism underlying HGF/c-MET mediated invasion in bladder cancer is partly addressed by this microarray dataset. HGF activates the canonical TGFb signaling...
3d
Contributors : Lei SUN ; Yen C LimSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo study the role of Ybx2 in brown fat activity, we performed the RNA-seq data for wildtype and Ybx2 knockout brown fat under room temperature and upon cold exposure as well as for wildtype and Ybx2 knockout brown adipocytes culture from stromal vascular fraction cells. To determine the targets of Ybx2, we performed RNA immunopercipitatoin followed by RNA-seq
3d
Contributors : AbuHammad Shatha ; Sheppard KarenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq was performed to compare the transcriptional programmes of A375 cells treated with Palbociclib or GSK3326595 compared to untreated cellsCyclin dependent kinase 4/6 (CDK4/6) inhibitors are an established treatment in estrogen receptor positive breast cancer and are currently in clinical development in melanoma; a tumour that exhibits high rates of CDK4 activation....
3d
Contributors : AbuHammad Shatha ; Sheppard KarenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq was performed to compare the transcriptional programmes of palbociclib-resistant A375 and CHL1 cells compared to their parental counterpartsCyclin dependent kinase 4/6 (CDK4/6) inhibitors are an established treatment in estrogen receptor positive breast cancer and are currently in clinical development in melanoma; a tumour that exhibits high rates of CDK4...
3d
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