Project description:Isocitrate dehydrogenase 2 (IDH2) mutations and its key effector 2-hydroxyglutarate (2-HG) have been reported to promote oncogenesis in various human cancers. To elucidate molecular mechanism(s) associated with IDH2 mutations, we established mouse embryonic fibroblasts (MEF) cells stably expressing cancer-associated IDH2R172S mutation and treated MEF cells with or without 2-HG. The expression of genes in these cells were analyzed by RNA-seq.

2021-09-13 | GSE180369 | GEO

RNA-seq analysis of MEF cells with stably overexpression of IDH2 mutation and MEF cells treated with 2-HG

Project description:RNA-seq analysis of MEF cells with stably overexpression of IDH2 mutation and MEF cells treated with 2-HG

| PRJNA748020 | ENA

ATAC sequencing of untreated and LLOMe treated MEF cells

Project description:ATAC sequencing of untreated and LLOMe treated MEF cells

| PRJEB83051 | ENA

RNA-seq of Paraquat-treated cells

Project description:RNA-seq of Paraquat-treated cells

| PRJNA632635 | ENA

RNA-seq of Bafilomycin-treated cells

Project description:RNA-seq of Bafilomycin-treated cells

| PRJNA632634 | ENA

RNA seq of HGPS treated cells

Project description:RNA seq of HGPS treated cells

| PRJEB21213 | ENA

RNA-Seq Analyses of the apoptosis and necroptosis in MEF

Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of MEF treated with PBS (control), TNF-ɑ + Cycloheximide (TC) or TNF-ɑ + Cycloheximide+ z-VAD-fmk (TCZ). The goals of this study are to compare the different gene expression profiles between MEF treated with TC compared to PBS treatment and MEF treated with TCZ compared to PBS treatment. Methods: In MEF, the combination of TNF-α and cycloheximide (TC) induces apoptosis, whereas the addition of z-VAD-fmk (TCZ) to this regimen promotes necroptosis, using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: By comparing the RPKM values between the two groups, a total 492 DEGs (342 upregulated and 150 downregulated) were identified in MEF treated with TC compared to PBS treatment, and a total 424 DEGs (242 upregulated and 182 downregulated) were identified in MEF treated with TCZ compared to PBS treatment. Next, we compared all identified DEGs in MEF between TC and TCZ treatment. We found that 252 DEGs overlapped between TC and TCZ treatment, whereas 240 DEGs were only present in TC treatment and 172 DEGs were only present in TCZ treatment. Conclusions: we firstly identified 492 DEGs in apoptotic MEF, and as well as 424 DEGs in necroptotic MEF. And we performed the enriched molecular pathway, molecules, transcription factors and signaling networks by IPA analysis. We revealed that apoptosis and necroptosis may share certain common canonical pathways and transcription factors.

2020-01-09 | GSE143294 | GEO

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