|
| Antibodies |
|
| RAD51 (D4B10) |
Cell Signaling |
Cat# 8875; RRID:AB_2721109 |
| RAD51 |
Abcam |
Cat# ab133534; RRID:AB_2722613 |
| Phospho-RAD51 (Tyr315) |
Thermo Fisher Scientific |
Cat# PA5-38699; RRID: AB_2555293 |
| ABL1 (8E9) |
BD Pharmingen |
Cat# 554148; RRID:AB_2220994 |
| CrkL (B-1) |
Santa Cruz |
Cat# sc-365092; RRID:AB_10847682 |
| Phospho-CrkL (Tyr207) |
Cell Signaling Technology |
Cat# 3181; RRID:AB_331068 |
| ABL2 (6D5) |
Novus Biologicals |
Cat# H00000027-M03; RRID: AB_828506 |
| RAD52 |
Proteintech |
Cat# 28045-1-AP; RRID:AB_2881046 |
| Phospho-RAD52 (Tyr104) |
Thermo Fisher Scientific |
Cat# PA5-105172; RRID:AB_2816645 |
| Phospho-RAD52 (Tyr104) |
Sigma |
Cat# SAB4504265 |
| Phospho-Histone H2A.X (Ser139) (20E3) |
Cell Signaling Technology |
Cat# 9718; RRID:AB_2118009 |
| Histone H2A.X (D17A3) |
Cell Signaling Technology |
Cat# 7631; RRID:AB_10860771 |
| Vinculin (E1E9V) |
Cell Signaling Technology |
Cat# 13901; RRID:AB_2728768 |
| Beta-Tubulin |
Cell Signaling Technology |
Cat# 2146; RRID:AB_2210545 |
| Beta-Actin (8H10D10) |
Cell Signaling Technology |
Cat# 3700; RRID: AB_2242334 |
| Cleaved PARP (Asp214) (D64E10) |
Cell Signaling Technology |
Cat# 5625; RRID: AB_10699459 |
| Cleaved Caspase 3 (Asp175) |
Cell Signaling Technology |
Cat# 9661; RRID: AB_2341188 |
| Chk1 |
Cell Signaling Technology |
Cat# 2360; RRID:AB_2080320 |
| Phosphor-Chk1 (S345) |
Cell Signaling Technology |
Cat# 2341; RRID: AB_330023 |
| Phosphotyrosine (4G10) |
Millipore Sigma |
Cat# 05-321; RRID: AB_309678 |
| Anti-BrdU (Rat) |
Abcam |
Cat# ab6326; RRID:AB_305426 |
| Anti-BrdU (Mouse) |
BD Biosciences |
Cat# 347580; RRID:AB_10015219 |
| GFP (5G4) |
Cell Signaling |
Cat# 55494; RRID: AB_3101977 |
| FLAG (M2)-magnetic beads |
Millipore Sigma |
Cat#F8823; RRID:AB_2637089 |
| S9.6 |
Millipore Sigma |
Cat# MABE1095; RRID: AB_2861387 |
| PCNA (Rabbit) |
Abcam |
Cat# ab18197; RRID: AB_444313 |
| PCNA (Mouse) |
Millipore Sigma |
Cat# NA03; RRID: AB_2160355 |
| RNA Polymerase II/POL2RA pSer2 |
Novus Biologicals |
Cat# NB100-1805; RRID: AB_10001499 |
| Peroxidase AffiniPure Goat Anti-Rabbit IgG (H + L) |
Jackson Immunoresearch |
Cat#111-035-003; RRID:AB_2313567 |
| Peroxidase AffiniPure Goat Anti-Mouse IgG (H + L) |
Jackson Immunoresearch |
Cat# 115-035-003; RRID:AB_10015289 |
| Alexa Fluor-488-goat anti-Mouse IgG (H + L) antibody |
Thermo Fisher Invitrogen |
Cat# A11001; RRID: AB_2534069 |
| Alexa Fluor-568-goat anti-Rabbit IgG (H + L) antibody |
Thermo Fisher Invitrogen |
Cat# A11011; RRID: AB_143157 |
| Alexa Fluor-594-goat anti-Rat-IgG |
Thermo Fisher Invitrogen |
Cat# A11007; RRID:AB_141374 |
| Alexa Fluor 647-goat anti-Rabbit IgG (H + L) antibody |
Thermo Fisher Invitrogen |
Cat# A21244; RRID: AB_2535812 |
|
| Chemicals, Peptides, and Recombinant Proteins |
|
| GNF-5 (Abl kinase small molecule inhibitor) |
Duke Small Molecule Synthesis Facility |
N/A |
| ABL001 (Asciminib) |
Duke Small Molecule Synthesis Facility |
N/A |
| Berzosertib (VE-822, VX970, M6620) |
Selleckchem |
Cat# 7102 |
| DRB (5,6-Dichloro-1-β-D-ribofuranosylbenzimidazole |
Sigma |
Cat# 287891 |
| Doxycycline Hyclate |
Millipore Sigma |
Cat# D5207 |
| Fugene 6 |
Promega |
Cat# E2692 |
| Fugene HD |
Promega |
Cat# E2311 |
| Lipofectamine 2000 |
Invitrogen |
Cat# 1668-027 |
| 5-Chloro-2'-deoxyuridine (CldU) |
Sigma |
Cat# C6891 |
| Iododeoxyuridine (IdU) |
Sigma |
Cat# I7125 |
| D-Luciferin potassium |
Thermo Fisher |
L2916 |
| Isoflurane |
Duke CCIF pharmacy (Covetrus) |
NDC: 11695-6777-2 |
| Protein A/G plus-agarose |
Sanat Cruz Biotechnology |
Cat# sc-2003 |
| Polybrene |
Sigma |
Cat# TR-1003-G |
| RNase H1 |
New England Biolabs |
Cat# M0297S |
| RNase III |
New England Biolabs |
Cat# M0245S |
| RNase T1 |
Thermo Fisher |
Cat# EN0541 |
| Tamoxifen |
Sigma |
Cat# T2859 |
| Hydroxyurea |
Sigma |
Cat# H8627 |
| High-Fidelity 2× Master Mix Q5 polymerase |
New England Biolabs |
Cat# M0492 |
| T4 Polynucleotide Kinase |
New England Biolabs |
Cat# M0201 |
| T4 ligase |
New England Biolabs |
Cat# M0202 |
| DpnI |
New England Biolabs |
Cat# R0176 |
| PaqCI |
New England Biolabs |
Cat# R0745 |
| Quick CIP |
New England Biolabs |
Cat# M0525 |
| rSAP |
New England Biolabs |
Cat# R0745 |
| AscI |
New England Biolabs |
Cat# R0558 |
| AgeI-HF |
New England Biolabs |
Cat# R3552 |
| EcoRI-HF |
New England Biolabs |
Cat# R3101 |
| NotI-HF |
New England Biolabs |
Cat# R3189 |
| Stbl3 E. Coli |
Thermo Fisher |
Cat# C737303 |
|
Mix & Go! E.coli Transformation kit |
Zymo Research |
Cat# T3001 |
| Oligo dT |
Thermo Fisher |
Cat# 18418012 |
| M-MLV |
Thermo Fisher |
Cat# 28025013 |
| RNaseOut |
Thermo Fisher |
Cat# 10777019 |
| iTaq Universal SYBR |
Bio-Rad |
Cat# 1725121 |
| Mounting medium for IF |
Invitrogen |
Cat# P36941
|
| Matrigel |
Corning |
Cat# CB-40234A |
|
| Critical Commercial Assays |
|
| Cell Titer Glo |
Promega |
Cat# G7571 |
| RNeasy RNA purification kit |
Qiagen |
Cat# 74104 |
| 4% paraformaldehyde solution |
Thermo Fisher |
Cat# J61889, AP |
| Duolink®
In Situ Red Starter Kit Mouse/Rabbit |
Sigma-Aldrich |
Cat# DUO92101 |
| Duolink®
In Situ PLA® Probe Anti-Mouse PLUS |
Sigma-Aldrich |
Cat# DUO92001 |
| Duolink®
In Situ PLA® Probe Anti-Mouse MINUS |
Sigma-Aldrich |
Cat# DUO92004 |
| Duolink®
In Situ PLA® Probe Anti-Rabbit PLUS |
Sigma-Aldrich |
Cat# DUO92002 |
| Duolink®
In Situ PLA® Probe Anti-Rabbit MINUS |
Sigma-Aldrich |
Cat# DUO92005 |
| Duolink®
In Situ Wash Buffers, Fluorescence |
Sigma-Aldrich |
Cat# DUO82049 |
| Duolink In Situ mounting medium with DAPI |
Sigma-Aldrich |
Cat# DUO82040 |
| Duolink Antibody Diluent (1×) |
Sigma-Aldrich |
Cat# DUO82008 |
|
| Deposited Data |
|
| H69 control versus GNF5 treated cells RNA-seq |
This paper |
GEO: GSE289452
|
|
| Experimental Models: Cell Lines |
|
| NCI-H69 |
ATCC/Duke University Cell Culture Facility |
Cat# HTB-119; RRID: CVCL_1579 |
| NCI-H146 |
ATCC/Duke University Cell Culture Facility |
Cat# HTB-173; RRID: CVCL_1473 |
| NCI-H2171 |
ATCC/Duke University Cell Culture Facility |
CAT# CRL-5929; RRID: CVCL_1536 |
| NCI-H1048 |
ATCC/Duke University Cell Culture Facility |
CAT# CRL-5853; RRID: CVCL_1453 |
| NCI-H82 |
ATCC/Duke University Cell Culture Facility |
CAT# HTP-175; RRID: CVCL_1591 |
| DMS53 |
ATCC/Duke University Cell Culture Facility |
Cat# CRL-2062; RRID: CVCL_1177 |
| U2OS |
ATCC |
Cat# HTB-96; RRID: CVCL_0042 |
| HEK-293T |
ATCC |
Cat# CRL-3216; RRID: CVCL_0063 |
|
| Experimental Models: Organisms/Strains |
|
| Outbred athymic nu/nu mice |
Jackson Laboratory |
Cat#007850, RRID: IMSR_JAX:007850 |
|
| Oligonucleotides |
|
| See Table S2 for a list of all primers and oligonucleotides |
|
| Recombinant DNA |
|
| pReceiver-M35 |
GeneCopoeia |
Cat# EX-B0087-M35 |
| pReceiver-Lv203 (RAD51-WT) |
GeneCopoeia |
Cat# EX-B0087-Lv203 |
| CS-B0087-Lv203-01 (RAD51-Y315F) |
GeneCopoeia |
Cat# CS-B0087-Lv203-01 |
| pEGFP-C1-RAD52 (WT) |
a gift from the lab of Dr. Li Lan |
N/A |
| pEGFP-C1-RAD52 (Y104F) |
This paper |
N/A |
| N174-MCS-Puro vector |
a gift from the lab of Dr. Adam Karpf |
Addgene Cat# 81068 |
| N174-GFP-RAD52(WT) |
This paper |
N/A |
| N174-GFP-RAD52(Y104F) |
This paper |
N/A |
| N174-huABL1(shRNA_Res)-WT-HA-Clover-Neo |
This paper |
N/A |
| N174-huABL1(shRNA_Res)-K290R-HA-Clover-Neo |
This paper |
N/A |
| pN1-EGFP Vector |
This Lab |
N/A |
| pN1-EGFP-mABL-WT |
This Lab |
N/A |
| pN1-EGFP-mABL-PP (PPEE) |
This Lab |
N/A |
| pN1-EGFP-mABL-KM (K790M) |
This Lab |
N/A |
| pLKO-puro shRAD51 (UTR) |
Duke Functional Genomics Shared Resource Facility |
TRCN0000018875 |
| pLKO-puro shRAD52 (UTR) |
Sigma Mission (Shclnd) |
TRCN0000271415 |
| ER-AsiSI |
Tanya T. Paull 2014 paper |
- |
| pCDNA-ABL1 PP |
(Plattner et al., 2004) |
N/A |
|
| Software and Algorithms |
|
| Prism 9 |
Graphpad |
http://graphpad.com/scientific-software/prism
|
| ImageJ |
Schneider et al., 2012 |
http://imagej.nih.gov
|
| Living Image |
Perkin Elmer |
http://perkinelmer.com
|
| Flowjo Portal |
- |
https//flowjo.com.portal
|
| Kaplan-Meier plot |
- |
https://doi.org/10.1111/bph.16257
|
| GSEA 3.0 |
Subramanian et al., 2005
|
http://software.broadinstitute.org/gsea
|
