iMEF SDHC-loss RNA-seq time course. Mus musculus

We have developed a tet-inducible immortalized mouse embryonic fibroblast (iMEF) cell culture model of SDH-loss paraganglioma/pheochromocytoma in which silencing gene rearrangement of the Sdhc floxed allele is driven by doxycycline-dependent expression of cre-recombinase from a tet-inducible promoter (R26M2rtTA/+;TetOcre;Sdhcfl/fl). Using this model and an isogenic Sdhc wt control line (R26M2rtTA/+;TetOcre;Sdhcfl/wt), we have characterized the time-course of Sdhc gene rearrangement, protein loss, and succinate accumulation following induction with doxycycline. Using RNA-seq, we have quantified changes in gene expression due to succinate accumulation using our Sdhc -/- cell line. Through a time-course experimental design, we have grown R26M2rtTA/+;TetOcre;Sdhcfl/fl (experimental) and R26M2rtTA/+;TetOcre;Sdhcfl/wt (control) iMEFs in standard DMEM media containing 10% FBS and quantified transcriptional changes in these cells as a function of time after triggering SDHC gene rearrangement via doxycycline exposure. Overall design: Included in this dataset are single replicate RNA-seq time course data for experimental (R26M2rtTA/+;TetOcre;Sdhcfl/fl) and control (R26M2rtTA/+;TetOcre;Sdhcfl/wt) cell lines at days 0, 5, 9, 12, and 20 after induction with doxycycline. We also include biological triplicate data for both experimental and control cell lines at day 16 after induction with doxycycline.

我们构建了一种四环素诱导型（tet-inducible）永生化小鼠胚胎成纤维细胞（immortalized mouse embryonic fibroblast, iMEF）培养模型，用于模拟SDH缺失型副神经节瘤/嗜铬细胞瘤。该模型中，Sdhc floxed等位基因的沉默性基因重排，由基于四环素诱导型启动子（tet-inducible promoter）表达的cre重组酶（cre-recombinase）的多西环素（doxycycline）依赖性表达所驱动，具体基因型为R26M2rtTA/+;TetOcre;Sdhcfl/fl。我们利用该模型及其同基因Sdhc野生型（Sdhc wt）对照细胞系（基因型为R26M2rtTA/+;TetOcre;Sdhcfl/wt），表征了经多西环素诱导后，Sdhc基因重排、蛋白丢失及琥珀酸积累的时间进程。我们借助RNA测序（RNA-seq）技术，利用本研究中的Sdhc纯合缺失（Sdhc-/-）细胞系，量化了琥珀酸积累所介导的基因表达变化。通过时间梯度实验设计，我们在含10%胎牛血清（FBS）的标准达尔伯克改良伊格尔培养基（DMEM）中培养了基因型为R26M2rtTA/+;TetOcre;Sdhcfl/fl的实验组iMEF细胞，以及基因型为R26M2rtTA/+;TetOcre;Sdhcfl/wt的对照组iMEF细胞，并量化了经多西环素触发SDHC基因重排后，细胞转录组随时间的变化情况。
数据集整体实验设计如下：本数据集包含实验组（R26M2rtTA/+;TetOcre;Sdhcfl/fl）与对照组（R26M2rtTA/+;TetOcre;Sdhcfl/wt）细胞系在多西环素诱导后第0、5、9、12及20天的单次重复RNA-seq时间进程数据；此外还收录了两类细胞系在多西环素诱导后第16天的生物学重复样本数据（每组3次重复）。