REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
p-IKK s180	Santa Cruz	sc-23470; RRID: AB_2122159
IKKα	Merck Millipore	OP133; RRID: AB_10681621
IKKα	Abcam	ab32041; RRID: AB_733070
IKKα(p45)	Merck Millipore	MABF222; RRID: not available
p-Chk1 S345	Cell Signaling	#2348; RRID: AB_331212
Chk1	Cell Signaling	#2360; RRID: AB_2080320
p-KAP1 S824	Bethyl Laboratories	A300-767A; RRID: AB_669740
KAP1	Cell Signaling	#4123; RRID: AB_2256670
ɣH2A.X	Cell Signaling	#2577; RRID: AB_2118010
ɣH2A.X	Merck Millipore	05-636; RRID: AB_309864
p-ERK 1/2	Cell Signaling	#4370; RRID: AB_2315112
ERK 1/2	Cell Signaling	#4696; RRID: AB_390780
Histone H3	Abcam	ab1791; RRID: AB_302613
Lamin B	Santa Cruz	sc-6216; RRID: AB_648156
α-Tubulin	Sigma	T6074; RRID: AB_477582
IKKβ	Abcam	ab32135; RRID: AB_733071
NEMO	Santa Cruz	sc-8330; RRID: AB_2124846
Cleaved caspase 3	Cell Signaling	#9661; RRID: AB_2341188
p-ATM S1981	Merck Millipore	05-740; RRID: AB_309954
p-53BP1 S1618	Cell Signaling	#6209; RRID: AB_11220229
53BP1	Abcam	ab21083; RRID: AB_722496
Anti-Rabbit-HRP (2ary)	DAKO	P0448; RRID: AB_2617138
Anti-Mouse-HRP (2ary)	DAKO	P0260; RRID: AB_2636929
Anti-Goat-HRP (2ary)	DAKO	P0449; RRID: AB_2617143
53BP1	Bethyl Laboratories	A300-272A; RRID: AB_185520
RIF1	Santa Cruz	sc-65191; RRID: AB_2126820
Alexa Fluor 488 donkey anti-rabbit (2ary)	Invitrogen	A21206; RRID: AB_141708
Alexa Fluor 488 donkey anti-mouse (2ary)	Invitrogen	A21202; RRID: AB_141607
Alexa Fluor 546 donkey anti-rabbit (2ary)	Invitrogen	A10040; RRID: AB_2534016
Alexa Fluor 546 donkey anti-goat (2ary)	Invitrogen	A11056; RRID: AB_142628
ATM	Santa Cruz	sc-135663; RRID: AB_2062962
Biological Samples
PDXIMIM#1-6	Hospital del Mar (Barcelona)	N/A
Chemicals, Peptides, and Recombinant Proteins
DMEM	Sigma	N/A
Advanced DMEM/F12	GIBCO	12634028
AZ628 (BRAFi)	Selleckchem	S2746
Vemurafenib	Selleckchem	S1267
Sorafenib	Selleckchem	S7397
5Z-7-oxozeaneol (TAKi)	Selleckchem	499610
Trametinib (MEKi)	Selleckchem	S2673
5-Fluorouracil (5-FU)	Accord	606544.3
Irinotecan	Frasenius Kabi	687014.3
Doxorubicin	Accord	174247
Matrigel®	Corning	354234
1x B27 supplement	GIBCO	17504044
1x N-2 supplement	GIBCO	17502048
Y-27632 (ROCK inhibitor)	Sigma	Y0503
EGF	Sigma	E9644
Human Noggin	PeproTech	120-10C
Human R-spondin 1	PeproTech	120-38
Nicotinamide	Sigma	N3376
A8301 (ALK inhibitor)	Sigma	SML0788
SB202190	Sigma	S70677
Prostaglandin E2	Tocris	2296
Gastrin I human	Tocris	3006
Ad-GFP	Vector Biolabs	1060
Ad-GFP-Cre	Vector Biolabs	1700
PhosSTOP phosphatase inhibitor cocktail	Roche	PHOSS-RO
Complete Mini protease inhibitor cocktail	Roche	11-836-170-001
TAMRA-TelG 5′-(TTAGGG)3-3′ PNA probe	PNA Bio-synthesis	F1006
Critical Commercial Assays
Envision+ System HRP Labeled Polymer anti-Rabbit	DAKO	K4003
Envision+ System HRP Labeled Polymer anti-Mouse	DAKO	K4001
3,3′-diaminobenzidine (DAB)	DAKO	K3468
ProLong. Diamond with DAPI	Thermo Scientific	P36971
ECL solution	Biological Industries	20-500-120
ECL Prime Western Blotting Detection Reagent	GE Healthcare	RPN2232
CometAssay Kit	Trevigen	4250-050-K
DharmaFECT 1 transfection reagent	Dharmacon	T-2001-03
Deposited Data
MS data from shC and shIKKα in UV/non-UV HT29 cells	PRIDE EBI-EMBL	PXD008932
Raw data from our manuscript is available at http://dx.doi.org/10.17632/k6xkjc2bf7.2	N/A	N/A
Experimental Models: Cell Lines
HT29	ATCC	HTB-38D
WiDr	ATCC	CCL-218
HCT116	ATCC	CCL-247
LIM1215	ECACC	10092301
DLD1	ATCC	CCL-221
SW480	ATCC	CCL-228
MCF7	ATCC	HTB-22
T24	ATCC	HTB-4
SKMEL131	ATCC	N/A
RWP1	ATCC	N/A
Mouse Embryonic Fibroblasts p38α KO	Gift from A. Nebreda.	N/A
Mouse Embryonic Fibroblasts Trf2FL/FL	Gift from T. de Lange.	N/A
Experimental Models: Organisms/Strains
Athymic nude, nu/nu mice	Jackson Laboratories	002019
Oligonucleotides
ON-TARGETplus SMART pool siRNA Chuk	Dharmacon	SO-2621140G
ON-TARGETplus Non-targeting Control Pool	Dharmacon	D-001810-10
MISSION shRNA, TRCN0000000508 (human) (shIKKα 1)	Sigma	N/A
MISSION shRNA, TRCN0000199496 (human) (shIKKα 4)	Sigma	N/A
TRC2 pLKO.5-puro Nonmammalian shRNA Control	Sigma	SHC202
MISSION shRNA, TRCN00001897 (human) (shIKKβ)	Sigma	N/A
MISSION shRNA, TRCN000022146 (human) (shNEMO)	Sigma	N/A
Recombinant DNA
pMD2.G plasmid	Addgene	#12259
pCMV-dR8.2 dvpr plasmid (human)	Addgene	#8455
Software and Algorithms
GraphPad Prism 6	Graphpad	https://www.graphpad.com/
Volocity 6.3	PerkinElmer	http://cellularimaging.perkinelmer.com/downloads/detail.php?id=14