|
Antibodies
|
| Mouse anti-STAG2 (Western blot) |
Santa Cruz |
Cat#sc-81852; RRID: AB_2199948 |
| Rabbit anti-STAG2 (ChIP-seq) |
Cell Signaling |
Cat#5882; RRID:AB_10834529 |
| Rabbit anti-STAG1(Western blot) |
Bethyl |
Cat# A302-579A;RRID:AB_2034857 |
| Rabbit anti-STAG1(ChIP-seq) |
Bethyl |
Cat# A302-578A; RRID:AB_2034858 |
| Rabbit anti-SMC1A |
Bethyl |
Cat# A300-055A; RRID:AB_2192467 |
| Rabbit anti-RAD21 |
Bethyl |
Cat# A300-080A; RRID:AB_2176615 |
| Rabbit anti-SMC3 |
Bethyl |
Cat# A300-060A, RRID:AB_67579 |
| Rabbit anti-H3K27me3 |
Cell Signaling |
Cat# 4395, RRID:AB_11220433 |
| Rabbit anti-EWS/FLI1 |
Abcam |
Cat# ab15289; RRID:AB_301825 |
| Rabbit anti -alpha TUBULIN |
Cell Signaling |
Cat# 2144; RRID:AB_2210548 |
| Mouse anti-GAPDH |
Santa Cruz |
Cat# sc-47724; RRID:AB_627678 |
| Rabbit anti-H3K27ac3 |
Abcam |
Cat# ab4729, RRID:AB_2118291 |
| Rabbit anti-POU3F2 |
Cell Signaling |
Cat# 12137; RRID:AB_2797827 |
| Rabbit anti-NR2F1 |
Cell Signaling |
Cat# 6364; RRID:AB_11220432 |
| Normal Rabbit IgG-R |
Cell Signaling |
Cat# 2729; RRID:AB_1031062 |
| Drosophila H2Az(spike-in Antibody) |
Active Motif |
Cat#61686; RRID: AB_2737370 |
| Rat anti-MouseIgG2a HRP conjugated secondary |
GenWay |
Cat# 25-783-70745;RRID:AB_1028627 |
| Sheep Anti-Mouse IgG ECL Antibody, HRP Conjugated |
GE Healthcare |
Cat# NA9310-1ml; RRID:AB_772193 |
|
Chemicals, Peptides, and Recombinant Proteins
|
| Bovine serum albumin |
Sigma-Aldrich |
Cat#F2442 |
| Phosphate Buffer Saline |
DFCI supply center |
NA |
| RPMI medium |
DFCI supply center |
NA |
| DMEM medium |
DFCI supply center |
NA |
| Penicillin-Streptomycin |
Gibco |
Cat#15070063 |
| Sodium Pyruvate |
ThermoFisher |
Cat#21051040 |
| Puromycin |
Gibco |
Cat#A1113802 |
| Polybrene |
American Bio |
Cat#AB01643 |
| TransIT-VirusGEN transfection reagent |
Mirus |
Cat#MIR 6704 |
| X-tremeGENE™ HP DNA Transfection Reagent |
Sigma |
Cat#6366236001 |
| ClonaCell-TCS medium |
Stem Cells |
Cat#03814 |
| MTT labeling reagent |
Sigma |
Cat#11 465 007 001 |
| Trypan Blue |
Gibco |
Cat#15250061 |
| Cell titer Glo |
Promega |
Cat#G7570 |
| 4′,6-diamidino-2-phenylindole (DAPI) |
Sigma |
Cat#D9542 |
| Pierce IP Lysis Buffer |
Thermofisher |
Cat#87788 |
| 16% methanol-free Formaldehyde solution (w/v) |
Thermofisher |
Cat#28908 |
| 5M NaCl |
Thermofisher |
Cat#AM9760G |
| Tris-EDTA pH 8.0 |
Sigma-Aldrich |
Cat#93283 |
| Ultrapure 0.5M EDTA |
Invitrogen |
Cat#15575-038 |
| Ultrapure 1M Tris-HCl pH 8.0 |
Invitrogen |
Cat#15568-025 |
| Ultrapure 10% SDS |
Invitrogen |
Cat#15553-035 |
| 2.5M Glycine solution |
BostonBioProducts |
Cat#C-4375 |
| Halt protease inhibitors |
Thermofisher |
Cat#78429 |
| phenylmethylsulfonyl fluoride (PMSF) |
Sigma-Aldrich |
Cat#P7626 |
| Transposase,TAGMENT DNA Enzyme |
Illumina |
Cat#15027865 |
| Dynabeads Protein A |
Invitrogen |
Cat#10004D |
| Lithium Chloride |
Sigma |
Cat#L9650 |
| NP40 |
Fisher |
Cat#FNN021 |
| Deoxycholic acid |
Fisher |
Cat#BP349-100 |
| NaHCO3 |
Sigma |
Cat#S5761 |
| NaN3 |
USB |
Cat#21610 |
| Triton X-100 |
Sigma |
Cat#0992-93-1 |
| Igepal CA-630 |
Sigma |
Cat#I8896 |
| Agencourt AMPure XP |
Beckman Coulter |
Cat#A63881 |
|
Critical Commercial Assays
|
| qScript cDNA synthesis Kit |
QuantaBio |
Cat#95047-025 |
| SYBR Green FastMix |
QuantaBio |
Cat#95072-250 |
| Click-iT™ Plus EdU Flow Cytometry Assay Kit |
Thermofisher |
Cat#C10634
|
| Subcellular Protein Fractionation Kit |
Thermofisher |
Cat#87787 |
|
Deposited Data
|
| ChIP-Seq, RNA-Seq, ATAC-Seq, Hi-ChIP |
This study |
GEO:GSE116495
|
| Ewing sarcoma Proteome |
This study |
http://massive.ucsd.eduMSV000082954
|
| Ewing sarcoma RNA-Seq |
(Crompton et al., 2014) |
dbGaP: phs000804.v1.p1 |
| Ewing sarcoma ChIP-Seq |
(Riggi et al., 2014) |
GEO: GSE61953
|
| Ewing sarcoma ChIP-Seq, RNA-seq |
(Tomazou et al., 2015) |
http://tomazou2015.computational-epigenetics.org
|
| Ewing sarcoma ChIP-Seq |
(Kojic et al., 2018) |
GEO: GSE101921
|
| Ewing sarcoma ChIP-Seq |
ENCODE: ENCSR000DZP |
GEO: GSM935376
|
| Ewing sarcoma Affymetrix arrays |
(Postel-Vinay et al., 2012) |
GEO: GSE34620
|
| Ewing sarcoma Affymetrix arrays |
(Savola et al., 2011) |
GEO: GSE17618
|
| Ewing sarcoma RNA-Seq |
(Smith et al., 2006) |
GEO: GSE53066
|
| Ewing sarcoma RNA-Seq |
(Sankar et al., 2014) |
NCBI: PRJNA176544 |
| Ewing sarcoma Affymetrix arrays |
(Smith et al., 2006) |
Array Express: E-GEOD-4560 |
| Ewing sarcoma RNA-Seq |
(He et al., 2017) |
GEO: GSE73092
|
| Ewing sarcoma IC-EwS gene signature |
(Aynaud, 2020) |
https://www.sciencedirect.com/science/article/pii/S2211124720300747?via=ihub
|
|
Experimental Models: Organisms/Strains
|
| Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) |
The Jackson Laboratory |
Cat# JAX:005557;RRID:IMSR_JAX:005557 |
| Zebrafish: Tg(nacre−/−; roy−/−)(Caspers) |
Dr. Leonard Zon Lab, DFCI |
NA |
|
Experimental Models: Cell Lines
|
| Human: A673 (Female) |
Dr. Todd Golub Lab, Broad Institute |
NA |
| Human: TC71 (Male) |
Dr. Todd Golub Lab, Broad Institute |
NA |
| Human: TC32 (Female) |
Dr. Todd Golub Lab, Broad Institute |
NA |
| Human: EW8 (Male) |
Dr. Todd Golub Lab, Broad Institute |
NA |
| Human: SKPNDW (Male) |
DR. Alejandro Sweet-Cordero Lab, Stanford University |
NA |
|
Oligonucleotides
|
| sgSTAG2#1 gRNA AATGTCTTACTGCTCTACAA |
IDT |
NA |
| sgSTAG2#4 gRNA GCTGAATGTCATCCTCCCGT |
IDT |
NA |
| sgSTAG1#2 gRNA GGAATTAGAGGAGCAGGCCG |
IDT |
NA |
| sgSTAG2#3 gRNA CAGCGAGCTTGAAGAAACAG |
IDT |
NA |
| sgNT1 gRNA GTAGCGAACGTGTCCGGCGT |
IDT |
NA |
| sgNT2 gRNA GACCGGAACGATCTCGCGTA |
IDT |
NA |
| sgPOU3F2-A gRNA GCTGTAGTGGTTAGACGCTG |
IDT |
NA |
| sgNR2F1-A gRNA GTACTGGCCTGGATTGGGCT |
IDT |
NA |
| sgLACZ gRNA AACGGCGGATTGACCGTAAT |
IDT |
NA |
|
Recombinant DNA
|
| pVSVg (addGene 8454) |
addGene |
RRID:Addgene_8454 |
| pPAX2 (addGene 19319) |
addGene |
RRID:Addgene_1226 |
| lentiCRISPR v2 |
addGene |
RRID:Addgene_52961 |
| pSpCas9BB-2A-GFP(PX458) |
addGene |
RRID:Addgene_48138 |
| CMV-GFP-T2A-Luciferase plasmid |
SBI |
Cat#BLIV101PA-1 |
|
Software and Algorithms
|
| Prism 8 |
Graphpad |
http://www.graphpad.com
|
| FlowJo V9.9.6 |
Tree Star |
http://www.flowjo.com/
|
| ImageQuant TL 8.2 |
Cytiva |
https://www.cytivalifesciences.com
|
