KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Antibodies used for immunoblotting and immunoprecipitation | N/A | See Table S1 |
| Antibodies used for ChIP | N/A | See Table S1 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| HALT PROTEASE AND PHOSPHATASE inhibitors | Pierce | Cat#PI78445 |
| Dynabeads® Protein G | LIFE TECHNOLOGIES | Cat#10004D |
| Biotinylated isoxazole (b-isox) | SIGMA ALDRICH | Cat#T511617–1MG |
| PDGF-BB | PeproTech | Cat#50589827 |
| TransIT-LT1 Transfection Reagent | MIRUS BIO LLC | Cat#MIR 2305 |
| Polybrene (HEXADIMETHRINE BROMIDE) | Sigma-Aldrich | Cat#H9268–50G |
| Puromycin | FISHER SCIENTIFIC | Cat#NC9138068 |
| Blasticidin | FISHER SCIENTIFIC | Cat#NC9016621 |
| Western Lightning Western Blot Chemiluminescence Reagent Plus | PERKINELMER | Cat#NEL104001EA |
| AUTORAD BLUE FILM | FISHER SCIENTIFIC | Cat#NC9648989 |
| RNase A | ROCHE | Cat#11119915001 |
| Proteinase K | LIFE TECHNOLOGIES | Cat#25530049 |
| Palbociclib (PD 0332991 ISETHIONATE) | SIGMA ALDRICH | Cat#PZ0199 |
| PRESCISSION PROTEASE | FISHER SCIENTIFIC | Cat#45001319 |
| GLUTATHIONE SEPHAROSE 4B | FISHER SCIENTIFIC | Cat#45000139 |
| D(+)TREHALOSE | SIGMA ALDRICH | Cat#T9531 |
| Critical Commercial Assays | ||
| TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set A | Illumina | Cat#RS-122–2301 |
| TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set B | Illumina | Cat#RS-122–2302 |
| Nextera DNA Sample Preparation Kit | Illumina | Cat#FC-121–1030 |
| Nucleospin RNA Plus | Clontech | Cat#740984.50 |
| Celltiter-Glo Luminescent cell viability assay | Promega | Cat#G7570 |
| fast SYBR Green Master Mix | ThermoFisher | Cat#4385618 |
| High Capacity cDNA reverse transcription kit | ThermoFisher | Cat#4387406 |
| Deposited Data | ||
| ChIP-seq, RNA-seq, ATAC-seq data | This study | GEO: GSE94278 |
| Raw and analyzed data | Riggi et al., 2014 | GEO: GSE61953 |
| Experimental Models: Cell Lines | ||
| A673 | ATCC | CRL-1598 |
| SK-N-MC | ATCC | HTB-10 |
| U20S | ATCC | HTB-96 |
| HEK293-T | ATCC | CRL-11268 |
| HEK293-T LentiX | Clontech | Cat#632180 |
| Human pediatric Mesenchymal Stem Cells | This study | N/A |
| Experimental Models: Organisms/Strains | ||
| BL21(DE3)LYSS | FISHER SCIENTIFIC | Cat#PRL1195 |
| Oligonucleotides | ||
| Primers for RT-qPCR | IDT | See Table S1 |
| Primers for ChIP-qPCR | IDT | See Table S1 |
| Recombinant DNA | ||
| pLIV-V5-EWS-FLI1 | This study | N/A |
| pLIV-V5-FLI1 | This study | N/A |
| N106-BAF47-FLI1 | This study | N/A |
| pLIV-HA-EWSR1 | This study | N/A |
| N106-GFP-EWSR1 | This study | N/A |
| pLIV-V5-EWS(YS12)-FL11 | This study | N/A |
| pLIV-V5-EWS(YS37)-FL11 | This study | N/A |
| pLIV-V5-SYGQ1-FLI1 | This study | N/A |
| pLIV-V5-SYGQ2-FLI1 | This study | N/A |
| pLIV-V5-EWS(ASYGQ1)-FLI1 | This study | N/A |
| pLIV-V5-EWS(ASYGQ2)-FLI1 | This study | N/A |
| pLIV-V5-EWS(DSYGQ1 DSYGQ2)-FLI1 | This study | N/A |
| pLIV-V5-EWS N-terminal | This study | N/A |
| pLIV-V5-FLI1 C-terminal | This study | N/A |
| pINDUCER-GFP | This study | N/A |
| pINDUCER- V5-EWS-FLI1 | This study | N/A |
| pINDUCER- EWS(YS37)-FLI1 | This study | N/A |
| pINDUCER- SYGQ2-FLI1 | This study | N/A |
| pGEX-6P1-V5-EWS-FLI1 | This study | N/A |
| pGEX-6P1-V5-FLI1 | This study | N/A |
| pGEX-6P1 - V5-EWS(YS37)-FLI1 | This study | N/A |
| pGEX-6P1 - V5-SYGQ1-FLI1 | This study | N/A |
| shRNA targeting sequence: BRG1 GGCATAGGCCTTAGCAGTAAC | Broad Institute | Clone ID: TRCN0000231102 |
| shRNA targeting sequence: BRG1 CTTTGCGTATCGCGGCTTTAA | Broad Institute | Clone ID: TRCN0000231101 |
| shRNA targeting sequence: BAF155#1 CCCACCACATTTACCCATATT | Broad Institute | Clone ID: TRCN0000015629 |
| shRNA targeting sequence: BAF155#2 GCAGGATATTAGCTCCTTATA | Broad Institute | Clone ID: TRCN0000015628 |
| shRNA targeting sequence: EWS-FLI1 CGTCATGTTCTGGTTTGAGAT | Broad Institute | Clone ID: TRCN0000005322 |
| Software and Algorithms | ||
| bwa | Li and Durbin, 2009 | https://github.com/lh3/bwa |
| bwtool | Pohl and Beato, 2014 | https://github.com/CRG-Barcelona/bwtool |
| STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| MACS2 | Zhang et al., 2008 | https://github.com/taoliu/MACS |
| Prism 6 | Graphpad | N/A |
| R | version 3.2.3 | https://cran.r-project.org |
| IGV | IGV_2.3.60 | https://github.com/igvteam/igv |
| HOMER | Heinz et al., 2010 | http://homer.salk.edu/homer/ |
| DESeq2 | Love et al., 2014 | https://bioc.ism.ac.jp/packages/3.1/bioc/html/DESeq2.html |
| bedtools | Quinlan and Hall, 2010 | https://github.com/arq5x/bedtools |
| featureCounts | Liao et al., 2014 | http://subread.sourceforge.net |
| ImageJ v1.50i Other | National Institutes of Health, USA | http://imagej.nih.gov/ij |
| Other | ||