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High throughput RNA sequencing of hepatocellular carcinoma and pre tumor samples from Tdg fl/-; UBC-cre/ERT2+ mice livers and their age/sex matched Tdg fl/fl controls livers

ABSTRACT: High throughput RNA sequencing of hepatocellular carcinoma and pre tumor samples from Tdg fl/-; UBC-cre/ERT2+ mice livers and their age/sex matched Tdg fl/fl controls livers

PROVIDER: PRJNA610508 | ENA |

REPOSITORIES: ENA

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High throughput RNA sequencing of hepatocellular carcinoma and pre tumor samples from Tdg fl/-; UBC-cre/ERT2+ mice livers and their age/sex matched Tdg fl/fl controls livers

Project description:We isolated whole livers from male TDG knockout livers (4-month post tamoxifen injection) and HCC, along with their age matched male control livers. RNA was extracted from the samples as per RNAzol manufacturer guidelines with DNase treatment. RNA was then analyzed by bioanalyzer and subjected to sequencing using the Illumina NextSeq 500 platform.

2020-03-06 | GSE146401 | GEO

Naïve and LCMV Cl13 infected liver tissue of ERT2 AlbCre Ifnar1 fl/fl mice

Project description:Age- and sex-matched (male, 2-3 months old) ERT2 AlbCre Ifnar fl/fl and ERT2 AlbCre Ifnar +/+ mice were injected intraperitoneally with 40 mg/kg tamoxifen for 5 consective days. Mice were then intravenously infected with 2x10^6 focus forming units of LCMV Cl13 and liver tissue of either genotype was harvested 1.5 days post infection and analyzed for transcriptomic changes (n = 3). Liver tissue of uninfected animals of both genotypes was harvested as control (n = 3).

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Next Generation Sequencing analysis of Hes1+/+ Cre-ERT2 and Hes1fl/fl Cre-ERT2 bone marrow derived macrophages transcriptomes.

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2013-09-05 | E-GEOD-46981 | biostudies-arrayexpress

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Next Generation Sequencing analysis of Hes1+/+ Cre-ERT2 and Hes1fl/fl Cre-ERT2 bone marrow derived macrophages transcriptomes.

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Gadd45a promotes DNA demethylation through TDG

Project description:Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA glycosylase (TDG) which has recently been shown to excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) generated in Ten-eleven-translocation (Tet) -initiated oxidative demethylation. The connection of Gadd45a with oxidative demethylation is evidenced by the enhanced activation of a methylated reporter gene in HEK293T cells expressing Gadd45a in combination with catalytically active TDG and Tet. Gadd45a interacts with TDG physically and increases the removal of 5fC and 5caC from genomic and transfected plasmid DNA by TDG. Knockout of both Gadd45a and Gadd45b from mouse ES cells leads to hypermethylation of specific genomic loci most of which are also targets of TDG and show 5fC enrichment in TDG-deficient cells. These observations indicate that the demethylation effect of Gadd45a is mediated by TDG activity. This finding thus unites Gadd45a with the recently defined Tet-initiated demethylation pathway. The dataset includes RRBS anlysis of 2 WT ES cell samples and 2 Gadd45a/b DKO ES cell samples.

2015-05-07 | E-GEOD-62496 | biostudies-arrayexpress

Gene expression profile in livers from control or Wy-14643 treated MycF/F or MycF/F,ERT2-Cre mice

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