KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
LanthaScreen Elite Tb-anti-His Antibody	Thermo Fisher Scientific	Cat:PV5863
LanthaScreen Tb-anti-GST-antibody	Thermo Fisher Scientific	Cat:PV3550
Bacterial and Virus Strains
BL21(DE3) E. coli cells	New England Biolabs	Cat:C2527
Biological Samples
HEK293T	ATCC	Cat:CRL-3216
3T3-L1 fibroblasts	ATCC	Cat:CL-173
Chemicals, Peptides, and Recombinant Proteins
9-cis Retinoic Acid	Cayman Chemical	Cat:14587
Ammonium Chloride, 99%15N	Cambridge Isotope Labs	Cat:NLM-467
Deuterium Oxide, 99.9% D	Sigma-Aldrich	Cat:151882
Dimethyl Sulfoxide-d6, 99.9% D	Cambridge Isotope Labs	Cat:DLM-10
Fluorescein Isothiocyanate Isomer I	Sigma-Aldrich	Cat:4274
HiLoad 16/600 Superdex 75 pg column	GE Healthcare Life Sciences	Cat:28989333
HiLoad 16/600 Superdex 200 pg column	GE Healthcare Life Sciences	Cat:28989335
HisTrap HP Ni NTA column	GE Healthcare Life Sciences	Cat:17–5248-02
Hypersil GOLD C8 LC column	Thermo Fisher Scientific	Cat:25205
Hypersil GOLD C18 LC column	Thermo Fisher Scientific	Cat:25012
Oil Red dye	Sigma-Aldrich	Cat:O0625
Rosiglitazone	Sigma-Aldrich	Cat:R2408
SR11023	Made by T.M.K.	Patent: WO2012170561 – US2012/0303769
GST-PPARγ-LBD	Thermo Fisher Scientific	Cat:PV4545
GST-PPARα-LBD	Thermo Fisher Scientific	Cat:PV4691
Cdk5/p35 kinase	Milipore	Cat: 14–477
Fluormone Pan-PPAR Green	Thermo Fisher Scientific	Cat:PV4896
3-iso-butyl-1-methylxanthine	Sigma-Aldrich	Cat:I7018
Dexamethasone	Sigma-Aldrich	Cat:D4902
Insulin	Sigma-Aldrich	Cat:I9278
X-treme Gene 9 transfection reagent	Sigma-Aldrich	Cat: 6365779001
SYBR green fluorescent dye	Bio-Rad	Cat: 1725271
TR-FRET Nuclear receptor buffer F	Thermo Fisher Scientific	Cat: PV4547
Pepsin column	(Busby et al., 2007)	http://www.sciencedirect.com/science/article/pii/S1387380606004040
C8 trap column, 1 mm x 10 mm	Thermo Scientific	Cat:25205–011001
Betasil C8 column, 5 μ 10×1 mm	Thermo Scientific	Cat:25203–051030
DTT	Sigma	Cat:10708984001
Iodoacetamide	Sigma	Cat:I1149
Trypsin	Promega	Cat:V5111
FITC-NH-ASKHKQLSELLRSGSS	LifeTein, LLC	N/A
FITC-NH-TNMGLEAIIRKALMGKYDQWEE	LifeTein, LLC	N/A
FITC-NH-LTERHKILHRLLQEGSPSD	LifeTein, LLC	N/A
FITC-NH-ASNLGLEDIIRKALMGSFD	LifeTein, LLC	N/A
NH-ASKHKQLSELLRSGSS	LifeTein, LLC	N/A
NH-TNMGLEAIIRKALMGKYDQWEE	LifeTein, LLC	N/A
NH-LTERHKILHRLLQEGSPSD	LifeTein, LLC	N/A
NH-ASNLGLEDIIRKALMGSFD	LifeTein, LLC	N/A
Spectra Multicolor Broad Range Protein Ladder	Thermo Fisher Scientific	Cat:26634
BS3 crosslinker	Thermo Fisher Scientific	Cat:21580
Chymotrypsin	Promega	Cat:V1061
Human PPARγ LBD, residues 231–505; isoform 2	(Hughes et al., 2012)	N/A
Human RXRα LBD, residues 223–462	(Kojetin et al., 2015)	N/A
PPARγ LBD crystal structure	(Nolte et al., 1998)	PDB code: 2PRG
Critical Commercial Assays
Qiazol reagent	Qiagen	Cat:79306
RNeasy Mini Kit	Qiagen	Cat:74104
LanthaScreen TR-FRET PPARγ competitive binding assay kit	Thermo Fisher Scientific	Cat:PV4893
High Capacity Reverse Transcription Kit	Applied Biosystems	Cat:4368814
HTScan CDK/Cyc kinase assay kit	Cell Signaling Technology	Cat:7519
RNeasy Mini Kit	Qiagen	Cat:74106
TruSeq stranded mRNA sample prep protocol	Illumina	Cat:RS-122–2101
Experimental Models: Cell Lines
HEK293T	ATCC	Cat:CRL-3216
3T3-L1 fibroblasts	ATCC	Cat:CL-173
Software and Algorithms
HDX Workbench	(Pascal et al., 2012)	http://hdxworkbench.com
Mascot	Matrix Science	http://www.matrixscience.com/
Plink2	Pfind Studio (Yang et al., 2012)	http://pfind.ict.ac.cn/software/pLink1/index.html
Deposited mass spectrometry raw data
XL-MS data	PRIDE (https://www.ebi.ac.uk/pride/archive/)	Accession number: PXD010222
HDX-MS data	Figshare (https://figshare.com)	https://figshare.com/s/d9fe41df3e945828e548
Other
Q Exactive Mass spectrometer	Thermo Fisher Scientific	Cat:IQLAAEGAAPFALGMAZR