Antibodies |
|
Mouse monoclonal anti-ARID2 (E-3) |
Santa Cruz |
sc-166117; RRID: AB_2060382
|
Rabbit monoclonal anti-ATM (D2E2) |
Cell Signaling Technology |
2873; RRID: AB_2062659
|
Rabbit polyclonal anti-Baf180 |
Millipore |
ABE70; RRID: AB_10807561
|
Rabbit polyclonal anti-BMI1 |
Bethyl Labs |
A301-694A; RRID: AB_1210891
|
Mouse monoclonal anti-BRG1 (G7) |
Santa Cruz |
sc-17796; RRID: AB_626762
|
Rabbit polyclonal anti-CENPF |
Bethyl Labs |
A301-611A; RRID: AB_1210906
|
Rabbit polyclonal anti-CTCF |
Millipore |
07-729; RRID: AB_441965
|
Rabbit polyclonal anti-Cyclin D1 |
Neomarkers |
RB-010-PO |
Rabbit polyclonal anti-Esco2 |
Abcam |
ab86003; RRID: AB_1924967
|
Rabbit monoclonal anti-EZH2 |
Cell Signaling Technology |
5246; RRID: AB_10694683
|
Mouse monoclonal anti-GFP (B2) |
Santa Cruz |
sc-9996; RRID: AB_627695
|
Mouse monoclonal anti-H2A-K119ub (E5C5) |
Millipore |
05-678; RRID: AB_309899
|
Rat monoclonal anti-NIPBL |
Abcam |
ab106768; RRID: AB_10859516
|
Rabbit polyclonal anti-PDS5A |
Abcam |
ab122352; RRID: AB_11129705
|
Rabbit polyclonal anti-PDS5B |
Abcam |
ab70298; RRID: AB_1269710
|
Rabbit polyclonal anti-Rad21 |
Abcam |
ab992; RRID: AB_2176601
|
Rabbit polyclonal anti-SMC3 |
Abcam |
ab155587 |
Goat polyclonal anti-SA1 |
Abcam |
ab4457; RRID: AB_2286589
|
Goat polyclonal anti-SA2 |
Abcam |
ab4463; RRID: AB_304471
|
Rabbit polyclonal anti-WAPL |
Abcam |
ab70741; RRID: AB_2216719
|
Mouse monoclonal anti-α-tubulin |
Abcam |
ab7291; RRID: AB_2241126
|
Mouse monoclonal anti-γ-H2AX (pSer139) (JBW301) |
Millipore |
05-636; RRID: AB_309864
|
Goat Anti-Rabbit Immunoglobulins/HRP |
Agilent (Dako) |
P044801-2 |
Rabbit Anti-Mouse Immunoglobulins/HRP |
Agilent (Dako) |
P026002-2; RRID: AB_2636929
|
Rabbit Anti-Goat Immunoglobulins/HRP |
Agilent (Dako) |
P044901-2 |
Goat Anti-Rat Immunoglobulins/HRP |
Millipore |
AP136P; RRID: AB_91300
|
Goat Anti-Mouse IgG/FITC |
Sigma-Aldrich |
F0257-1ML |
Sheep Anti-rabbit IgG/Cy3 |
Sigma-Aldrich |
C2306-1ML |
Goat Anti-Mouse IgG/Alexa Fluor 555 |
Thermo Fisher Scientific (Invitrogen) |
A-21422; RRID: AB_141822
|
|
Chemicals, Peptides, and Recombinant Proteins |
|
4-hydroxytamoxifen |
Sigma-Aldrich |
H7904-5MG |
5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) |
Sigma-Aldrich |
D1916-10MG |
ATM Kinase Inhibitor |
Santa Cruz Biotechnology |
sc-202963 (CAS 587871-26-9) |
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail |
Sigma-Aldrich (Roche Applied Science) |
04693159001 |
5α-Dihydrotestosterone (DHT) |
Sigma-Aldrich |
D-073-1ML |
Doxycycline hyclate |
Sigma-Aldrich |
D9891-G |
Hoechst 33258 solution |
Sigma-Aldrich |
94403-1ML |
Propidium iodide |
Thermo Fisher Scientific (Invitrogen) |
P3566 |
RNase A |
Sigma-Aldrich |
R5503-100MG |
Sheild1 |
Clontech Laboratories UK Ltd |
632189 |
Thymidine |
Sigma-Aldrich |
T1895-5G |
|
Critical Commercial Assays |
|
Click-iT RNA Alexa Fluor 594 Imaging Kit |
Thermo Fisher Scientific (Invitrogen) |
C10330 |
HiPerFect Transfection Reagent |
QIAGEN |
301705 |
Lipofectamine RNAiMAX Transfection Reagent |
Thermo Fisher Scientific (Invitrogen) |
13778150 |
Lipofectamine LTX Reagent with PLUS Reagent |
Thermo Fisher Scientific (Invitrogen) |
15338100 |
Nucleospin Tissue |
Machery-Nagel |
740952.5 |
Power SYBR green PCR master mix |
Thermo Fisher Scientific (Applied Biosystems) |
4367659 |
Premo FUCCI Cell Cycle Sensor (BacMam 2.0) |
Thermo Fisher Scientific (Invitrogen) |
P36237 |
QIAGEN RNeasy Mini Kit |
QIAGEN |
74106 |
QuikChange II Site-Directed Mutagenesis Kit |
Agilent |
200523 |
SuperScript First-Strand Synthesis System for RT-PCR |
Thermo Fisher Scientific (Invitrogen) |
11904018 |
TurboFect Transfection Reagent |
Thermo Fisher Scientific |
R0531 |
TMPRSS2/ERG Deletion/Breakapart Probe |
Cytocell |
LPS 021 |
|
Deposited Data |
|
Differential exome sequencing data and files |
This paper |
SAMN08226046 |
Human reference genome NCBI build 37, GRCh37 |
Genome Reference Consortium |
https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
Genomic data commons |
Grossman, 2016 |
N/A |
COSMIC database |
Forbes et al., 2017 |
https://cancer.sanger.ac.uk |
Raw data files deposited in Mendeley Data |
This paper |
https://doi.org/10.17632/4h486ty62f.1 |
|
Experimental Models: Cell Lines |
|
U2OS |
From cell line stocks at GDSC, Sussex University, validated by STR profiling with ECACC |
N/A |
U2OS 263 IFII |
Gift from Roger Greenberg; Tang et al., 2013
|
N/A |
U2OS 265 |
Gift from Roger Greenberg; Tang et al., 2013
|
N/A |
LNCaP clone FGC |
ATCC |
CRL-1740 |
U2OS Baf180 KO CRISPR Clone 15 |
This paper |
N/A |
U2OS NTC sh |
Hopkins et al., 2016 |
N/A |
U2OS Baf180 sh |
Hopkins et al., 2016 |
N/A |
|
Oligonucleotides |
|
siRNA sequence: ARID2 SMARTpool: ON-TARGETplus |
Dharmacon |
L-026945-01-0005 |
siRNA sequence: Baf180 SMARTpool: ON-TARGETplus |
Dharmacon |
L-008692-01-0005 |
siRNA sequence: BRG1 SMARTpool: ON-TARGETplus |
Dharmacon |
L-010431-00-0005 |
siRNA sequence: BRM SMARTpool: ON-TARGETplus |
Dharmacon |
L-017253-00-0005 |
siRNA sequence: CTCF SMARTpool: ON-TARGETplus |
Dharmacon |
L-020165-00-0005 |
siRNA sequence: Esco2 SMARTpool: ON-TARGETplus |
Dharmacon |
L-025788-01-0005 |
siRNA sequence: NIPBL SMARTpool: ON-TARGETplus |
Dharmacon |
L-012980-00-0005 |
siRNA sequence: NTC: Non-targeting pool: ON-TARGETplus |
Dharmacon |
D-001810-10-20 |
siRNA sequence: Rad21 SMARTpool: ON-TARGETplus |
Dharmacon |
L-006832-00-0005 |
siRNA sequence: SMC3 SMARTpool: ON-TARGETplus |
Dharmacon |
L-006834-00-0005 |
siRNA sequences for ATM, NTC, PDS5A, PDS5B, Sororin, STAG1, STAG2, WAPL, see Table S4
|
This paper |
N/A |
Primer: TMPRSS2_rtPCR FWD: CTGGTGGCTGATAGGGGAT |
Lin et al., 2009 |
N/A |
Primer: TMPRSS2_rtPCR REV: GTCTGCCCTCATTTGTCGAT |
Lin et al., 2009 |
N/A |
Primer: TMPRSS2-CR-3F: CACCGTTCATTCACGATCCCTAACA |
Li et al., 2018 |
N/A |
Primer: TMPRSS2-CR-3R: AAACTGTTAGGGATCGTGAATGAAC |
Li et al., 2018 |
N/A |
Primer: ERG-CR-2F: CACCGGGATGGTAAACGGAGAGTGC |
Li et al., 2018 |
N/A |
Primer: ERG-CR-2R: AAACGCACTCTCCGTTTACCATCCC |
Li et al., 2018 |
N/A |
Primer: TMPRSS2:ERG FWD: AGCGCGGCAGGAAGCCTTAT |
Sigma |
N/A |
Primer: TMPRSS2:ERG REV: CCGTAGGCACACTCAAACAACGA |
Mani, 2016 |
N/A |
Primer: Reporter Transcript FWD: TCATTAGATCCTGAGAACTTCA |
Shanbhag et al., 2010 |
N/A |
Primer: Reporter Transcript REV: TTTTGGCAGAGGGAAAAAGA |
Shanbhag et al., 2010 |
N/A |
Primer: Actin_rtPCR FWD: GCTCGTCGTCGACAACGGCTC |
Lin et al., 2009 |
N/A |
Primer: Actin_rtPCR REV: CAAACATGATCTGGGTCATCTTCTC |
Lin et al., 2009 |
N/A |
Primer: cyclophilin A_rtPCR FWD: CTGGACCCAACACAAATGGT |
This paper |
N/A |
Primer: cyclophilin A_rtPCR REV: GCCTTCTTTCACTTTGCCAAAC |
This paper |
N/A |
Primer: Sororin_rtPCR FWD: AGTCTCGCCAGTGGTGTGCT |
Zhang, 2011 |
N/A |
Primer: Sororin_rtPCR REV: TTCAACCAGGAGATCAAACTGC |
Zhang, 2011 |
N/A |
Primer: GAPDH_rtPCR FWD: ACATCGCTCAGACACCATG |
Meisenberg, 2015 |
N/A |
Primer: GAPDH_rtPCR REV: TGTAGTTGAGGTCAATGAAGGG |
Meisenberg, 2015 |
N/A |
Primers for Site Directed Mutagenesis and creation of Rad21-pEGFP-C1 and STAG2-pmRFP-C1, see Table S4
|
This paper |
N/A |
|
Recombinant DNA |
|
Plasmid: Baf180-pEGFP-C3 |
Kakarougkas et al., 2014 |
N/A |
Plasmid: STAG2-pEGFP-C1 |
Solomon, 2011 |
Addgene plasmid: 31972 |
Plasmid: STAG2-pmRFP-C1 |
This paper |
N/A |
Plasmid: Rad21-pEGFP-C1 |
This paper |
N/A |
Plasmid: pEGFP-C1 |
Gift from Keith Caldecott (University of Sussex) |
N/A |
Plasmid: pmRFP-C1 |
Gift from Keith Caldecott (University of Sussex) |
N/A |
Plasmid: Cas9-gRNA |
Horizon |
free CRISPR guide program |
pcDNA4-GFP-IRES-Puro |
Gift from Keith Caldecott (University of Sussex) |
N/A |
pSpCas9(BB)-2A-Puro (PX459) V2.0 |
Gift from Helfrid Hochegger (University of Sussex) |
N/A |