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Series GSE68845 Query DataSets for GSE68845
Status Public on Mar 09, 2018
Title BRCA1, R-loops and Recombination defects in Ewing's sarcoma (DRIP-seq)
Organism Homo sapiens
Experiment type Other
Summary Ewing’s sarcoma family of tumors (ESFT) is an aggressive pediatric bone and soft tissue cancer. It is the prototypical example of mesenchymal tumors driven by a fusion oncogene involving the ewing sarcoma break point region 1 (EWSR1) gene, most frequently– EWS-FLI1. We have discovered that loss of EWSR1 leads to accumulation of R-loops, replication stress and impaired homologous recombination, recapitulating breast cancer 1, early onset (BRCA1) deficiency. EWS-FLI1 acts dominant negatively in ESFT to impart the same phenotypes. Further we demonstrate that in ESFT, BRCA1 predominantly associates with the elongating transcription machinery and is unavailable for DNA strand break repair. Gene expression profiling identified upregulated compensatory mechanisms in ESFT cells to process increased R-loops (RNASEH2 and FEN1) and replication stress (Fanconi Anemia). Taken together, our data identifies BRCA1 sequestration due to transcription stress as the mechanistic basis for ESFT chemosensitivity and suggests potential targets for the much lacking second-line therapy.
Overall design Examination of R-loops was conducted using DRIP-Seq. Three different Ewing's sarcoma cell lines, IMR90 control cell line and U2OS cells transfected with either siRNA against EWSR1 or EWS-FLI1 vector along with appropriate controls were used.Samples were further treated with either vehicle or LD65 dose of etoposide for 6 hours. Genomic DNA was extracted, digested with a restriction enzyme cocktail and used for pulldown of DNA:RNA hybrids.
Contributor(s) Gorthi A, Yidong C, Bishop AJ
Citation(s) 29513652
Submission date May 13, 2015
Last update date May 15, 2019
Contact name Yidong Chen
Phone 2105629163
Organization name UT Health Science Center at San Antonio
Department Population Health Sciences
Street address 8403 Floyd Curl Drive, MSC 7784
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (26)
GSM1683483 TC32 NT DRIP
GSM1683484 TC32 Etop DRIP
GSM1683485 TC32 RNH
This SubSeries is part of SuperSeries:
GSE68847 BRCA1, R-loops and Recombination defects in Ewing's sarcoma
BioProject PRJNA283900
SRA SRP058311

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Supplementary file Size Download File type/resource
GSE68845_RAW.tar 8.1 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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