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| Status |
Public on Jun 28, 2022 |
| Title |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [CUT&RUN] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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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. RNA-seq of shHOXD13 defined HOXD13-ergulated genes, so we performed CUT&RUN for HOXD13 and histone marks (H3K27ac, H3K4me3, H3K4me1, and H3K27me3) to determine how it regulates target genes.
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| Overall design |
A673 and CHLA10 cells were run through the automated CUT&RUN protocol (Janssens et al. 2018 Methodology). In brief, 250,000-500,000 cells were collected and incubated with concavalin A beads for 10min. Cells were then washed and permeabilized with 0.05% digitonin wash buffer solution and incubated with primary antibodies for 24-48 hours at 4C. Samples were then run through the automated platform (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-ufeetje)
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| Contributor(s) |
Wu F, Apfelbaum A, Lawlor B |
| Citation(s) |
35653119 |
| Submission date |
Aug 20, 2021 |
| 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 (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (22)
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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 |
PRJNA756549 |
| SRA |
SRP333473 |
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