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| Status |
Public on Nov 21, 2017 |
| Title |
iMEF SDHC-loss RRBS time course |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
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 reduced representation bisulfite sequencing (RRBS), we have quantified changes in the genome-wide distribution of cytosine/5’-methyl-cytosine 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 DNA methylation changes in these cells as a function of time after triggering SDHC gene rearrangement via doxycycline exposure.
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| Overall design |
Included in this dataset are single replicate RRBS time course data for experimental (R26M2rtTA/+;TetOcre;Sdhcfl/fl) and control (R26M2rtTA/+;TetOcre;Sdhcfl/wt) cell lines at days 0, 5, 9, 12,16, and 20 after induction with doxycycline.
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| Contributor(s) |
Maher LJ, Smestad JA |
| Citation |
Smestad, J., Hamidi, O., Wang, L., Nelson Holte, M., Al Khazal, F., Erber, L., Chen, Y., and James Maher Iii, L. (2018). Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma. Oncotarget. 9:6109-6127. doi: 10.18632/oncotarget.23639.
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| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA166025 |
Molecular Basis of Familial Paraganglioma |
MAYO CLINIC |
LOUIS JAMES MAHER |
| F30 CA220660 |
Understanding succinate-induced global transcriptional and epigenetic reprogramming and identifying unique vulnerabilities intrinsic to SDH-deficient cells |
MAYO CLINIC |
John Andrew Smestad |
|
| Submission date |
Sep 07, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
John Andrew Smestad |
| Organization name |
Mayo Clinic
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Louis (Jim) Maher
|
| Street address |
200 1st St. SW
|
| City |
Rochester |
| State/province |
Minnesota |
| ZIP/Postal code |
55905 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE103663 |
Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma |
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| Relations |
| BioProject |
PRJNA402065 |
| SRA |
SRP117088 |
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