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| Status |
Public on Feb 15, 2018 |
| Title |
iMEF SDHC-loss ChIP-seq |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We have developed a tet-inducible immortalized mouse embryonic fibroblast (iMEF) cell culture system for studying the cross-talk between TCA cycle metabolism and the epigenome, 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 differences in H3K4me3, H3K27me3, and chromatin succinylation that occur genome-wide in response to SDHC loss. For these experiments, both cell lines were grown in standard DMEM media containing 10% FBS at 37˚C and 5% CO2. 16 days after induction of Sdhc gene rearrangement by doxycycline induction, chromatin from the respective lines was prepared and patterns of H3K4me3, H3K27me3, and chromatin succinylation were studied via ChIP-seq.
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| Overall design |
Included in this dataset are duplicate ChIP-seq experiments and input chromatin for experimental (R26M2rtTA/+;TetOcre;Sdhcfl/fl) and control (R26M2rtTA/+;TetOcre;Sdhcfl/wt) cell lines at day 16 after induction with doxycycline.
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| Contributor(s) |
Maher LJ, Smestad JA |
| Citation(s) |
29888767 |
| 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 |
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| |
| Submission date |
Sep 27, 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 (16)
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| This SubSeries is part of SuperSeries: |
| GSE129956 |
Functional genomics of iMEF SDHC-loss stable line |
|
| Relations |
| BioProject |
PRJNA412470 |
| SRA |
SRP119050 |
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