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Status |
Public on Jun 25, 2024 |
Title |
PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing Other
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Summary |
MYCN-amplified neuroblastoma cells exhibit upregulation of translation initiation factors as a result of MYCN-driven transcriptional amplification, including the RNA helicase eIF4A1. Here, we treated MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells with a novel translation initiation inhibitor, amidino-rocaglate CMLD12824, to analyze the impact on the global pattern of eIF4A1 binding to mRNA compared to the naive condition.
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Overall design |
MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells (COG-N-415) were treated for 1 hour with 10 nM CMLD12824 amidino-rocaglate compound and photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of eIF4A1 was performed to analyze the patterns and changes in eIF4A1 binding of cellular RNAs. Corresponding bulk RNA-sequencing was also performed as control.
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Contributor(s) |
Volegova M, Banerjee U, Brown L, John P Jr, George R |
Citation(s) |
38662542 |
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Submission date |
Mar 15, 2024 |
Last update date |
Jun 26, 2024 |
Contact name |
Marina Volegova |
E-mail(s) |
marina_volegova@dfci.harvard.edu
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Organization name |
Dana-Farber Cancer Institute
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Department |
Pediatric Oncology
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Lab |
George Lab
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Street address |
450 Brookline Ave
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
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Platforms (1) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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Samples (8)
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GSM8150896 |
COG415 cells solvent replicate 1 PAR-CLIP |
GSM8150897 |
COG415 cells solvent replicate 2 PAR-CLIP |
GSM8150898 |
COG415 cells CMLD12824 replicate 1 PAR-CLIP |
GSM8150899 |
COG415 cells CMLD12824 replicate 2 PAR-CLIP |
GSM8150900 |
COG415 cells solvent replicate 1 RNAseq |
GSM8150901 |
COG415 cells solvent replicate 2 RNAseq |
GSM8150902 |
COG415 cells CMLD12824 replicate 1 RNAseq |
GSM8150903 |
COG415 cells CMLD12824 replicate 2 RNAseq |
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Relations |
BioProject |
PRJNA1088607 |