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| Status |
Public on Feb 21, 2019 |
| Title |
Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI [Experiment 2] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The purpose of this study was to define unique classes of EWS/FLI target genes and the distinct set of structural features present in the EWS domain required for target gene regulation at different EWS/FLI response elements. This study reports the first genome-wide transcriptomic description of a partially-functional EWS/FLI mutant . We report new structure-function dependencies across different classes of response element and tie these dependencies to the ability of EWS/FLI to transform cells.
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| Overall design |
For knockdown of wildtype EWS/FLI and rescue with differing cDNAs in A673 Ewing sarcoma cell lines, shRNAs were retrovirally delivered on day 1. Selection in 2 µg/mL puromycin (Sigma P8833) occurred on days 2-5. Cells were infected with retrovirus containing the cDNA in the pMSCV-hygro backbone on day 5. Double selection in puromycin and 400 µg/mL hygromycin B (Thermo Fisher 10687010) began on day 6 and continued until day 16. Cells were subsequently harvested for RNA, protein, and seeded for soft agar assays.
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| Contributor(s) |
Theisen ER, Lessnick SL |
| Citation(s) |
30899417 |
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Emily R. Theisen, Kyle R. Miller, Iftekhar A. Showpnil, Cenny Taslim, Kathleen I. Pishas and Stephen L. Lessnick. Transcriptomic analysis functionally maps the intrinsically disordered domain of EWS/FLI and reveals novel transcriptional dependencies for oncogenesis. Genes & Cancer 2019;10(1-2). doi:10.18632/genesandcancer.188
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| Submission date |
Nov 14, 2018 |
| Last update date |
Mar 28, 2019 |
| Contact name |
Emily Rose Theisen |
| E-mail(s) |
emily.theisen@nationwidechildrens.org
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| Organization name |
Nationwide Children's Hospital
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| Department |
Center For Childhood Cancer and Blood Diseases
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| Street address |
700 Childrens Drive
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (21)
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| This SubSeries is part of SuperSeries: |
| GSE122537 |
Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI |
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| Relations |
| BioProject |
PRJNA505502 |
| SRA |
SRP168620 |
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