Table S1. List of the genes regulated by thyroid hormones in intestinal crypt cells

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1 Table S1. List of the genes regulated by thyroid hormones in intestinal crypt cells Probeset ID Gene symbol Cell adhesion/extracellular matrix Gene title Fold change a pvalue a WT THvsPTU T-Test TRa0/0 vs WT-C TRb-/- vs WT-C _at Tgfbi Transforming growth factor. beta induced NC NC _at Mgp Matrix Gla protein NC NC _at Gp1bb Glycoprotein Ib. beta polypeptide * I NC _at Cfh Complement component factor h NC D _at Fga Fibrinogen. alpha polypeptide * NC D _at Cldn8 Claudin D D _at Amn Amnionless * D D _a_at Afm Afamin * D D _a_at Ttr Transthyretin * NC D _at Dab1 Disabled homolog 1 (Drosophila * NC NC Cell cycle control/proliferation _s_at Ccnb1 Cyclin B NC NC _at Aurka Aurora kinase A NC NC _at Dock5 Dedicator of cytokinesis 5 * I I _s_at Sesn1 Sestrin NC NC _at Cdc2a Cell division cycle 2 homolog A (S. pombe) NC NC _at Bub1b Budding uninhibited by benzimidazoles NC NC homolog. b (S. cerevisiae) _a_at Tacc3 Transforming. acidic coiled-coil containing NC NC protein _at Mad2l1 MAD2 (mitotic arrest deficient. homolog)-like NC NC (yeast) _at Ube2c Ubiquitin-conjugating enzyme E2C NC NC _at Ccna2 Cyclin A I NC _at Cdkn1c Cyclin-dependent kinase inhibitor 1C (P57) -4, D D _a_at Cenph Centromere protein H NC NC _at Cdk8 Cyclin-dependent kinase 8 * NC D Cell Signaling _at sfrp2 Secreted frizzled-related protein NC I _at Tlr3 Toll-like receptor 3 $ NC I _at Gng10 Guanine nucleotide binding protein (G protein) NC NC gamma _at Notch1 Notch gene homolog 1 (Drosophila) 2 MS NC NC _at Notch2 Notch gene homolog 2 (Drosophila) NC NC _at Fzd2 Frizzled homolog 2 (Drosophila) NC NC _x_at Wnt5b Wingless-related MMTV integration site 5B $ NC I _at Dkk3 Dickkopf homolog 3 (Xenopus laevis) $ NC I _at Epha4 Eph receptor A4 $ NC I _at Dvl1 Dishevelled 1, dsh homolog (Drosophila) 1.5 MS NC NC Down- regulated _x_at Marcksl1 MARCKS-like NC NC

2 _a_at Rab30 RAB30. member RAS oncogene family NC D _x_at Ndrg N-myc downstream regulated gene NC NC _at Bmp7 Bone morphogenetic protein 7 * D D _a_at Edn1 Endothelin 1 * NC D _at Fgf1 Fibroblast growth factor NC NC _at Acvr1b Activin A receptor type 1B * NC NC _s_at Gli2 GLI-Kruppel family member GLI2 $ NC D _a_at Fgf12 Fibroblast growth factor 12 $ NC D _at Bmp2 Bone morphogenetic protein 2 * NC I _at Pgrmc2 Progesterone receptor membrane component NC NC _s_at Csf1r Colony stimulating factor 1 receptor * NC D _at Sel1 Sel-1 suppressor of lin-12-like (C. elegans) NC NC _a_at FgfRl1 Fibroblast growth factor receptor-like 1 $ NC D _a_at EgfR Epidermal growth factor receptor $ NC D _s_at FgfR1 Fibroblast growth factor receptor 1 $ NC D _s_at Rhoc Ras homolog gene family. member C * NC NC Membrane proteins/transporters _at Lbp Lipopolysaccharide binding protein NC NC _a_at Slc13a1 Solute carrier family 13 (sodium/sulphate NC NC symporters). member _at Cd14 CD14 antigen NC NC _s_at Il17re Interleukin 17 receptor E NC I _a_at Kcne3 Potassium voltage-gated channel. Isk-related NC NC subfamily. gene _a_at Higd1a HIG1 domain family. member 1A NC NC _s_at Steap1 Six transmembrane epithelial antigen of the NC NC prostate _x_at sec61g SEC61. gamma subunit NC NC _a_at Lrig1 Leucine-rich repeats and immunoglobulin-like NC NC domains _at Abce1 ATP-binding cassette. sub-family E (OABP). member NC NC _a_at Pdzk1ip1 PDZK1 interacting protein 1 * D D _at Slc6a3 Solute carrier family 6 (neurotransmitter transporter. dopamine). member NC D _at Anxa13 Annexin A NC NC _at Abcb1a ATP-binding cassette. sub-family B (MDR/TAP). * D D member 1A _a_at Armcx1 Armadillo repeat containing. X-linked 1 * NC D _at Ctns Cystinosis. Nephropathic NC D _at Ptprd Protein tyrosine phosphatase. receptor type. D NC NC _at Abcg2 ATP-binding cassette. sub-family G (WHITE). * NC D member _s_at Tgoln1 Trans-golgi network protein /// trans-golgi * D D network protein _at Slc18a1 Solute carrier family 18 (vesicular monoamine). member NC NC Metabolism _at Upp1 Uridine phosphorylase NC NC _at Galgt2 Galactosyl-N-acetylglucosaminylpolypeptidebeta-1, NC NC 4-N-acetylgalactosaminyltransferase

3 _at Letm1 Leucine zipper-ef-hand containing I NC transmembrane protein _a_at Psmb8 Proteosome (prosome, macropain) subunit, beta NC NC type _s_at Gfm1 G elongation factor mitochondrial 1 * I NC _at Paics Phosphoribosylaminoimidazole carboxylase * NC NC _a_at Cyb5r1 Cytochrome b5 reductase 1 * NC NC _x_at Pgd Phosphogluconate dehydrogenase * NC NC _at Pkm2 Pyruvate kinase. muscle NC NC _at D19Wsu12e DNA segment. Chr 19. Wayne State University NC NC 12. expressed _at Shmt2 Serine hydroxymethyl transferase 2 * NC D (mitochondrial) _at Mthfd2 Methylenetetrahydrofolate dehydrogenase (NAD+ * NC I dependent) _s_at Idh3a Isocitrate dehydrogenase 3 (NAD+) alpha * NC NC _at Dhrs7 Dehydrogenase/reductase (SDR family) member * NC NC _at Psma1 Proteasome (prosome. macropain) subunit. alpha NC NC type _at Ndufb3 NADH dehydrogenase (ubiquinone) 1 beta NC NC subcomplex _s_at Gsta1 Glutathione S-transferase. alpha 1 (Ya) NC NC _at Ucp2 Uncoupling protein 2 (mitochondrial. proton NC NC carrier) _a_at Mod1 Malic enzyme supernatant * NC NC _a_at March5 Membrane-associated ring finger (C3HC4) NC NC _at Abhd6 Abhydrolase domain containing NC NC _at Ndufa5 NADH dehydrogenase (ubiquinone) 1 alpha NC NC subcomplex, _at Elovl6 ELOVL family member 6. elongation of long NC NC chain fatty acids (yeast) _at Acss2 Acyl-CoA synthetase short-chain family member NC NC _at Cycs Cytochrome c. somatic * NC NC _a_at Umps Uridine monophosphate synthetase NC NC Down regulated _at Rdh7 Retinol dehydrogenase NC NC _at Aldh1a1 Aldehyde dehydrogenase family 1. subfamily A NC NC _at Acot1 Acyl-CoA thioesterase NC D _at Aldh1a7 Aldehyde dehydrogenase family 1. subfamily A I NC _s_at Gstm3 Glutathione S-transferase. mu NC D _a_at Hmgcs2 3-hydroxy-3-methylglutaryl-Coenzyme A NC NC synthase _at Vnn1 Vanin NC NC _at Stard5 StAR-related lipid transfer (START) domain NC NC containing _at Prkg2 Protein kinase. cgmp-dependent. type II * NC NC _at Ass1 Argininosuccinate synthetase NC NC _at Btd Biotinidase NC NC _a_at Faah Fatty acid amide hydrolase NC NC _x_at Cyp4f16 cytochrome P450. family 4. subfamily f. * NC NC polypeptide _at Pipox Pipecolic acid oxidase NC NC _at Nnt Nicotinamide nucleotide transhydrogenase NC NC _at Slc25a36 Solute carrier family 25. member 36 * D D _at Adh1 Alcohol dehydrogenase 1 (class I) NC NC _at Akr1c13 Aldo-keto reductase family 1. member C NC D _at Gstm4 Glutathione S-transferase. mu NC NC

4 _at Gyk Glycerol kinase NC NC _a_at Limk2 LIM motif-containing protein kinase 2 * NC NC _a_at Scpep1 Serine carboxypeptidase 1 * NC NC _x_at Aco1 Aconitase 1 * NC NC _at Acss1 Acyl-CoA synthetase short-chain family member NC NC _at Man1a Mannosidase 1. alpha NC D _at Gcnt2 Glucosaminyl (N-acetyl) transferase 2. I NC D branching enzyme _at Pank3 Pantothenate kinase 3 (Pank3), mrna NC NC _at Pklr Pyruvate kinase liver and red blood cell NC D _at Aldh6a1 Aldehyde dehydrogenase family 6. subfamily A NC NC _x_at Aldh18a1 Aldehyde dehydrogenase 18 family, member A NC I Nucleic Acid Metabolism _at Rbm14 RNA binding motif protein NC NC _at Pola1 Polymerase (DNA directed). alpha NC NC _at Apobec3 Apolipoprotein B editing complex NC NC _at Rrm1 Ribonucleotide reductase M NC NC _a_at Apobec1 Apolipoprotein B editing complex MS NC NC _at Piwil2 Piwi-like homolog 2 (Drosophila) * NC D _at Rnase4 Ribonuclease, RNase A family 4 * NC D Stress and apoptosis _a_at Hsp110 Heat shock protein NC NC _at Dffb DNA fragmentation factor. beta subunit $ I I _at Gpx2 Glutathione peroxidase NC NC _at Tnfrsf14 Tumor necrosis factor receptor superfamily. * I NC member _s_at Hspe1 Heat shock protein 1 (chaperonin 10) NC NC _at Hif3a Hypoxia inducible factor 3. alpha subunit NC NC _at Cat catalase NC D _at Sgk3 Serum/glucocorticoid regulated kinase 3 * NC D _at Ddit4 DNA-damage-inducible transcript I NC Transcriptional regulation _a_at Zbtb20 Zinc finger and BTB domain containing 20 $ I I _s_at Zfp654 Zinc finger protein NC NC _at Fos FBJ osteosarcoma oncogene NC I _at Hes2 Hairy and enhancer of split 2 (Drosophila) $ NC I _a_at Ctnnb1 Catenin (cadherin associated protein) beta NC I _a_at Surb7 SRB7 (suppressor of RNA polymerase B) NC NC homolog (S. cerevisiae) _at Asf1b ASF1 anti-silencing function 1 homolog B (S NC NC cerevisiae) _a_at Cenpa Centromere protein A NC NC _at Klf9 Kruppel-like factor 9 $ NC I _at Hes1 Hairy and enhancer of split 1 (Drosophila) 1.5 MS NC NC

5 _at Neurod1 Neurogenic differentiation NC NC _at Tcf23 Transcription factor NC D _at Tcfec Transcription factor EC * NC D _at FoxP1 Forkhead box P1. full insert sequence NC NC _a_at Sox10 SRY-box containing gene 10 $ NC D _at Cxxc5 CXXC finger NC NC _s_at Hnf4a Hepatic nuclear factor 4, alpha # NC NC _a_at Srebf1 Sterol regulatory element binding factor 1 # NC NC _a_at Nkx2-3 NK2 transcription factor related, locus 3 $ NC D (Drosophila) _at Cdx2 Caudal type homeo box 2 $ NC D _a_at Tcf4 Transcription factor 4 $ NC D Miscellaneous _at Sh3bgr SH3-binding domain glutamic acid-rich protein NC NC _at Gm1 Gene model 1, (NCBI) * NC NC _a_at Oact1 O-acyltransferase (membrane bound) domain NC NC containing _at Kif4 Kinesin family member NC NC _at Dnclc1 Dynein, cytoplasmic, light chain I NC _at Arpp19 camp-regulated phosphoprotein NC NC _a_at Cryz Crystallin. Zeta * NC NC _at Adamts1 A disintegrin-like and metallopeptidase with # NC I thrombospondin type 1 motif _at Ankmy2 Ankyrin repeat and MYND domain containing 2 # NC NC _a_at Dab2 Disabled homolog 2 (Drosophila) * NC NC _at Lrrc50 Leucine rich repeat containing NC NC _a_at Fmo5 Flavin containing monooxygenase 5 * NC NC _at Vat1 Vesicle amine transport protein 1 homolog (T NC NC californica) _at Pxmp4 Peroxisomal membrane protein NC D _at Spfh1 SPFH domain family. member NC NC _at Atp13a3 ATPase type 13A3 * NC NC a: we filtered for a pvalue<0.05 and a fold change of at least 50%. *: Comparison WT-TH vs WT-C $: Comparison TRb-/- vs WT-C; #: Comparison WT-PTU vs WT-C. NC: not changed; I: significantly increased; D: significantly decreased MS: marginally significant Cell cycle control/proliferation Transcriptional regulation Cell Signaling Nucleic Acid Metabolism Stress and apoptosis Metabolism Cell adhesion/extracellular matrix Membrane proteins/transporters