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| Status |
Public on Jun 28, 2022 |
| Title |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Posterior homeobox D genes, in particular HOXD13, are over-expressed by Ewing sarcoma, a tumor driven by the oncogenic fusion protein EWS-FLI1. Here, we have found that EWS-FLI1 maintains HOXD13 expression through a GGAA microsatellite enhancer in the developmental posterior HOXD regulatory domain. Activation of this enhancer is EWS-FLI1 dependent and epigenomic silencing of this region leads to loss of HOXD13 expression in Ewing sarcoma cells, but not in unrelated cells. To determine the function of HOXD13 activation in Ewing sarcoma we performed nascent RNA sequencing or RNA sequencing upon HOXD13 knockdown.
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| Overall design |
HOXD13 was knocked down by doxy-cycline inducible (0.5 ug/uL) shRNAs in two human Ewing sarcoma cell lines, CHLA10 and A673 for 72 hours. Three replicates each of targeting shRNA (shHOXD13 #1) and non-targeting control (shNS) were subject to nascent RNA sequencing (Bru-seq).
HOXD13 was knocked down by doxy-cycline inducible (0.5 ug/uL) shRNAs in the human Ewing sarcoma cell lines, TC32, for 72 hours. Three replicates each of targeting shRNA (shHOXD13 #1) and non-targeting control (shNS) were subject to RNA sequencing
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| Contributor(s) |
Apfelbaum A, Magnuson B, Ljungman M, Lawlor E |
| Citation(s) |
35653119 |
| Submission date |
Apr 10, 2020 |
| Last update date |
Jul 01, 2022 |
| Contact name |
April Apfelbaum |
| E-mail(s) |
aapfelba@umich.edu
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| Organization name |
University of Michigan, Seattle Childrens Research Institute
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| Department |
Cancer Biology Program
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| Lab |
Lawlor Lab
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| Street address |
1100 Olive Way Suite 100
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (18)
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| This SubSeries is part of SuperSeries: |
| GSE182513 |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma |
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| Relations |
| BioProject |
PRJNA624652 |
| SRA |
SRP256218 |
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