Our strategy was to manipulate mTOR signaling in vivo, then characterize the transcriptome and translating mRNA in liver tissue. In adult rats, we used the non-proliferative growth model of refeeding after a period of fasting, and the proliferative model of liver regeneration following partial hepatectomy. We also studied livers from pre-term fetal rats (embryonic day 19-20) in which fetal hepatocytes are asynchronously proliferating. All three models employed rapamycin to inhibit mTOR signaling.
Profiling of the fetal and adult rat liver transcriptome and translatome reveals discordant regulation by the mechanistic target of rapamycin (mTOR).
Specimen part, Time
View SamplesDownregulation of EZH2 Leads to Cellular Senescence with Features of SASP Overall design: Cells were infected with a lentivirus vector expressing shRNA against EZH2 and harvested at 4 and 8 days after infection. Total RNA was harvested from cells using Trizol reagent (Invitrogen) and further purified using the Purelink RNA Mini kit (Invitrogen) with DNase I digestion. RNA library preparation with polyA selection and Illumina HiSeq 2x150bp sequencing was performed by GeneWiz Inc. Paired-end reads were quality trimmed using Trim galore v0.4.0 and subsequently aligned to the human reference genome, hg19, using HISAT2 v2.1.0. Reads mapping to annotated genes were quantified using featureCounts (Liao et al., 2014). Differential gene expression was determined using DESeq2 v1.12.4 (Love et al., 2014) and significance was defined as FDR-corrected p-values of <0.05. The log2 fold change for each gene was used to rank the list of genes for GSEAPreranked analysis (Subramanian et al., 2005). FPKM values were calculated using DESeq2 and Z-scores were generated from FPKMs
Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage- and Histone Methylation-Dependent Pathways.
Subject, Time
View SamplesWe investigate the biological effects of radiation using Drosophila Melanogaster as a model organism, focusing on gene expression and lifespan analysis to determine the effect of different radiation doses. Our results support a threshold effect in response to radiation: no effect on lifespan and no permanent effect on gene expression is seen at doses below 10,000 Roentgens. Overall design: Adult male Drosophila were irradiated 2 days after eclosion, with one of 6 radiation doses: 10; 1,000; 5,000; 10,000; 20,000 Roentgens. Samples were taken at 3 time points (2, 10 and 20 days post-irradiation).
Drosophila melanogaster show a threshold effect in response to radiation.
Specimen part, Subject
View SamplesExpression data from four different lifespan-extending conditions: dietary restriction in two different genetic backgrounds (canton-s and a yw, w1118 combination), sir2 overexpression and p53 knockdown (+/-).
Comparative transcriptional profiling identifies takeout as a gene that regulates life span.
Sex, Age, Specimen part
View SamplesFeeding resveratrol to Drosophila melanogaster extends lifespan. Studies of microarray show similarities between calorie/dietary restriction and resveratrol on both a gene expression and biological pathway level.
Comparative transcriptional pathway bioinformatic analysis of dietary restriction, Sir2, p53 and resveratrol life span extension in Drosophila.
Sex, Age, Specimen part
View SamplesRecent work using mouse models has revealed that mTORC2, which unlike mTORC1 is not acutely sensitive to rapamycin, plays a key role in the regulation of organismal physiology. The substrates and pathways regulated by mTORC2 are at present relatively unknown
Hepatic signaling by the mechanistic target of rapamycin complex 2 (mTORC2).
Sex, Specimen part, Treatment
View SamplesMYC is a pleiotropic transcription factor that regulates numerous pathways and whose deregulation promotes cancer. Myc+/- mice have extended lifespan relative to their wild type littermates. To better understand the effects of the Myc+/- genotype on cellular processes, microarrays were performed on young (5 month) and old (24 month) Myc+/- and WT males in liver, skeletal muscle, and adipose tissues.
Reduced expression of MYC increases longevity and enhances healthspan.
Sex, Age, Specimen part
View SamplesIMR90 cells were passaged until replicative senescence and compared with proliferating cells. Overall design: We used RNA-Seq to detail the global programme of gene expression in human IMR90 replicative induced senescence
Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability.
No sample metadata fields
View SamplesIMR90 cells were infected with pLNC-RAS:ER (from Jesus Gil lab) with retroviral gene transfer. Infected cells were drug selected G418. The cells were induced either with ethanol as control or with 100nM final conc 4-hydroxytamoxifen (sigma H7904) for ectopic expression of protein Overall design: We used RNA-Seq to detail the global programme of gene expression in human IMR90 oncogene induced senescence
Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability.
No sample metadata fields
View SamplesIdentify shear and side-specific miRNAs in Human Aortic Valvular Endothelial Cells using the following conditions: 1) fHAVEC exposed to OS (FO), 2) vHAVEC exposed to OS (VO), 3) fHAVEC exposed to LS (FL), and 4) vHAVEC exposed to LS (VL).
Discovery of shear- and side-specific mRNAs and miRNAs in human aortic valvular endothelial cells.
Specimen part
View Samples