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1 Supplementry Figure 1 Ncor1 Expression Muscle Liver Lmi Ppropi Kindey Pncres Lung Testis Bone Mrrow Thymus Spleen Peripherl Lymph nods Smll Intestine Ncor1 Expression DN DP SP CD8 SP Supplementry Figure 1. Ncor1 expression profiles in different tissues nd thymocyte susets. () Quntittive RT-PCR nlysis of Ncor1 mrna expression in vrious tissues(n=3) nd () in the indicted thymocyte susets (n=3, repet 2 times) sorted using flow cytometry. DN, - CD8 - doulenegtive thymocytes; DP, + CD8 + doule-positive thymocytes; SP, + single-positive thymocytes; CD8 SP, CD8 + single-positive thymocytes.

2 Supplementry Figure 2 Ncor1 f/f CD8 Lck-Cre Ncor1 f/f Lck-Cre Thymocytes (%) DP SP CD8 SP Ncor1 f/f Lck-Cre Ncor1 f/f Lck-Cre Thymocytes (%) ** TCRβ P3 P4 P5 c d #5 5.8 # Ncor1 /f # # # dull CD8 dull (%) ** Lck-Cre # Ncor1 f/f Lck-Cre Ncor1 f/f Lck-Cre Ncor1 f/f Lck-Cre # #4.99 MHCI # CD8 Supplementry Figure 2. Thymocyte profiles in Ncor1 flox/flox, Lck-Cre nd Ncor1 flox/flox Lck-Cre mice. () Surfce expression of versus CD8 (up) nd versus TCRβ (down) on totl thymocytes (n=4 for ech group) detected y flow cytometry. () Quntifiction of different thymocyte susets in (). (c) Flow cytometry nlysis of 5 su-popultions (left) y MHCI nd expression on totl thymocytes (n=4 for ech group, respectively). The right pnel shows nd CD8 expression on gted popultion #3. (d) The proportion of dull CD8 dull susets in popultion #3. Sttisticl significnce ws nlysed using the two-tiled Student s t test (, not significnt; ** P<.1; P<.1).

3 Supplementry Figure CD8 4KO % of Thymocytes DP SP CD8 SP Supplementry Figure 3. Thymocyte profiles in Ncor1 flox/flox -Cre mice. () Surfce expression of nd CD8 on thymocytes from Ncor1 flox/flox -Cre (4KO) mice nd Ncor1 flox/flox () mice (n=3 to 5). () Quntifiction of different thymocyte susets in (). DP, + CD8 + doule-positive thymocytes; SP, + single-positive thymocytes; CD8 SP, CD8 + single-positive thymocytes. Dt re representtive of three independent experiments. Sttisticl significnce ws nlysed using the two-tiled Student s t test ( P<.1).

4 Supplementry Figure 4 % of Mx CD5 + (%) 3 ** 2 1 CD5 MFI (*1 3 ) 15 * 1 5 CD5 lo hi c % of Mx MFI 4 ** Supplementry Figure 4. CD5 nd expression in NCoR1-deficient thymocytes. () Flow cytometry nlysis of CD5 expression (left) on totl thymocytes from NCoR1-deficient () nd wild type () mice (n=3 to 5) nd quntifiction of the CD5-positive su-popultion (right). () Men fluorescence intensity of CD5 on lo nd hi DP + CD8 + doule-positive) thymocytes from (n=4) nd (n=4) mice. (c) The histogrm plot (left) nd the men fluorescence intensity (right) of expression on totl thymocytes from nd OT-II TCR-trnsgenic mice (n=3) detected y flow cytometry. Dt re representtive of two independent experiments. Sttisticl significnce ws nlysed using the two-tiled Student s t test (, not significnt, ** P<.1).

5 Supplementry Figure 5 Foxp Foxp3 + (%).5 ** Foxp3 + (%) SP c CD1d Tetrmer TCRβ CD1d Tetrmer + TCR + (%) Supplementry Figure 5. Development of oth Treg cells nd inkt cells is defective in the thymus of NCoR1-deficient mice. () Foxp3 expression in totl thymocytes from NCoR1-deficient () (n=7) nd wild type () (n=6) mice y intrcellulr stining (left) nd quntifiction of Foxp3 + cells (right). () Quntifiction of Foxp3 + cells in + single-positive ( SP) nd thymocytes in (). (c) CD1d Tetrmer nd TCRβ expression in totl thymocytes from (n=6) or (n=7) mice (left) y flow cytometry nd quntifiction of CD1d Tetrmer + TCRβ + cells (right). Sttisticl significnce ws nlysed using the two-tiled Student s t test (, not significnt; ** P<.1; P<.1)..

6 Supplementry Figure (min) p-plcγ1 PLCγ1 p-erk1/2 Erk p-p38 p38 β-ctin 155 kd 149 kd 44 kd 42 kd 44 kd 43 kd 4 kd 45 kd Supplementry Figure 6. TCR signling in NCoR1-deficient thymocytes. Immunolot nlysis of phosphorylted (p)-plc-γ1, p-erk1/2, p-p38 nd totl protein of PLC-γ1, Erk nd p38 in lystes from wild type () nd NCoR1-deficient () thymocytes without or with stimultion in vitro for the indicted mounts of time. β-ctin served s loding control. Dt re representtive of there independent experiments.

7 Supplementry Figure 7 MOCK TCRβ+CD MFI 2 ** Act. Csp3 - ** Act. Csp Act. Csp c MOCK TCRβ+CD28 d Annexin V PI Annexin V + PI ** 3(hr) 6(hr) 12(hr) ** 24(hr) Supplementry Figure 7. NCoR1-deficient thymocytes re prone to poptosis. () The surfce mrker nd intrcellulr stining of the ctive cspse-3 (Act.Csp.3) detected y flow cytometry in totl NCoR1-deficient () (n=3) nd wild type () (n=3) thymocytes stimulted or not with TCR β nd CD28 for 6 hr. () The men fluorescence intensity of expression in Act.Csp3 + nd Act.Csp3 - thymocytes in (). (c) Flow cytometric stining of Annexin V nd propidium iodide (PI) on nd thymocytes stimulted in vitro for 6 hr (n=3 to 5). (d) Quntifiction of the poptotic thymocytes shown in (c). Dt re representtive of two independent experiments. Sttisticl significnce ws nlysed using the two-tiled Student s t test (** P<.1; P<.1).

8 Supplementry Figure 8 CD3e(µg/ml) CD28(µg/ml) NCoR1 Bim Tuulin kd 25 kd 5 kd Bim Reltive Expression 5 ** p1+2 p4+5 Supplementry Figure 8. Bim expression in TCR signlling stimulted thymocytes in vitro nd in sorted non-ctivted nd ctivted thymocytes in vivo. () Bim protein levels in NCoR1-deficient () nd wild type () thymocytes stimulted with different concentrtions of nti-tcrβ. () Non-ctivted thymocytes (popultion 1 + 2, p1+2) nd ctivted thymocytes (popultion 4 + 5, p4+5) were sorted y the surfce expression of nd TCRβ on totl (n=7) nd (n=7) thymocytes ccording to the gting in Fig. 2. Bim mrna levels in these sorted thymocytes were nlysed y quntittive RT-PCR. Sttisticl significnce ws nlysed using the two-tiled Student s t test (, not significnt, ** P<.1; P<.1).

9 Supplementry Figure Fsl Expression * Tnf Expression UD UD * (hr) (hr) Tril Expression Bk Expression (hr) (hr) Supplementry Figure 9. Expression of propoptotic genes in enriched DP thymocytes. Quntittive RT-PCR nlysis of Fsl, Tnf, Tril, nd Bk mrna levels in enriched NCoR1-deficient () nd wild type () DP ( + CD8 + doule-positive) thymocytes ctivted in vitro for the indicted time points. Dt re representtive of two independent experiments with four mice per genotype. The numer indictes the p vlue. Sttisticl significnce ws nlysed using the two-tiled Student s t test

10 Supplementry Figure 1 Cells (%) Cells (%) Bim KO dko CD62L hi lo CD62L lo hi CD62L hi CD24 lo CD62L lo CD24 hi Supplementry Figure 1. Proportions of mture (CD62L hi lo or CD62L hi CD24 lo ) nd immture (CD62L lo hi or CD62L lo CD24 hi ) susets in (n=4), (n=4), Bim KO (n=4) nd dko (n=5) thymocytes. Flow cytometry nlysis nd gting of mture or immture susets were performed s shown in Fig. 6c., wild type;, NCoR1-deficient; dko, Ncor1 nd Bim doule knockout.sttisticl significnce ws nlysed using the two-tiled Student s t test (, not significnt).

11 Supplementry Figure CD Cells (%) CD8 Cells (*1 6 ) CD8 c d 2 ** Foxp3 SSA Foxp3 + (%) Supplementry Figure 11. Loss of NCoR1 reduces peripherl nd CD8 T cells in the spleen ut increses the proportion of Tregs. () The surfce expression of nd CD8 on NCoR1-deficient () (n=4) nd wild type () (n=4) splenocytes detected y flow cytometry. () The percentges (left) or numers (right) of nd CD8 T cells gted in (). Dt were generted from three independent experiments. (c) Intrcellulr expression of Foxp3 in + TCRβ + (n=6) nd (n=6) splenocytes detected y flow cytometry. (d) Quntifiction of the Foxp3 + + T cells in (c). Dt re representtive of three independent experiments with more thn three mice per group. Sttisticl significnce ws nlysed using the two-tiled Student s t test (** P<.1; P<.1).

12 Supplementry Figure 12 CD62L live cells singel cells lymocytes DAPI FCS-W FCS-A CD8 #4 #3 lo Vα2+ hi CD5+ #5 #1 CD24 #2 TCRβ Vα2 CD5 #2 #1 DAPI FCS-W Act. Csp3 lymocytes FCS-A #4 #5 dullcd8dull live cells MHCI singel cells #3:hiMHCI- #3 CD8 lymocytes FCS-A FCS-W Annexin V singel cells Act. Csp.3 c PI live cells 5.1 singel cells d lymocytes FCS-A CD1d Tetrmer live cells Foxp3 e singel cells lymocytes FCS-A FCS-W DAPI CD8 5.2 DAPI FCS-W TCR β Supplementry Figure 12. Gting strtegies for flow cytometry nlyses. Representive FACS plots showing: () Gting strtegy for, CD8,, TCRβ, CD5, nd Vα2 (for OTII ckground) expression. () Gting strtegy for intrcellulr Act.Csp.3 in himhci-dullcd8dull thymocytes. (c) Gting strtegy to detect poptosis of thymocytes stimulted in vitro.(d) Gting strtegy to nlyze thymocytes profiling in one mrrow chimers. (e) Gting strtegy to nlyze T regultory cells nd invrint nturl killer T cells in thymus.

13 Supplementry Figure 13 Fig. 5d nti-ncor1 Suppl. Fig. 6 nti-p-plcγ1 nti-erk Suppl. Fig. 8 nti-ncor1 nti-bim nti-plcγ1 nti-p-p38 nti-bim nti-p-erk1/2 nti-p38 nti-tuulin nti-tuulin nti-β-ctin Supplementry Figure 13. The uncropped scns of western lots from Figure 5, Supplemenry Figure 6 nd 8.

14 Supplementl Tle 1. Genes expressed differentilly in thymocytes y RNA-seq In stedy stte thymocytes Gene / (ex vivo) Gene / (ex vivo) log2(fold_chnge) log2(fold_chnge) Gm7125 infinite Adcy Gm6594 infinite Itg AC infinite Cxxc Gh infinite Als2cl AC infinite Mllt Sfn Cnn Sps Pdcd St3gl Cd Wnt St3gl Gm Slc Dusp Shis Ifngr Sem Tl1xr AB Cdk5r H2-K Bcl Fgf Mnl Pdi Dusp AC Slc Ccr Scd Slfn Cd H2-Q Pik3r Ephx Pik3cg.7227 Ctsw Gimp Nkg Ctsl Xrr Lig Jup Tesp Phld Tu Pqr Acg Ccnd Esyt Lfng Lt Cd Gpr Gm Rpl Sdc Nrp n-r5-8s Ntn Cd Smoc Gm

15 In ctivted thymocytes Gene KO/ (3h ctivtion) Gene KO/ (3h ctivtion) log2(fold_chnge) log2(fold_chnge) Gm7125 infinite B4glnt Gm6594 infinite Myc Ighv1-49 infinite Gm AC Slc Sfn Ccr Acoxl H2-K Tl1xr Fm Scd Ador Il12r Tnf Dusp Cxxc ERDR Evl Gimp Pdcd Bcl H2-Q Acg Cd Ptger Ifi27l Ldlr Cited Gimp Ld Grmd Tgp Bcl2l Egr Mr Xcl Mnl Lfng Ccnd Tnfrsf Ctsl Rgs Ccr Ccnd Irf n-r5-8s Cd Sh3gl Ntn Ap Icos Gm Gpr

16 Supplementl Tle 2. Antiodies Informtion Antiodies for Flow cytometry nlysis Antiody Clone Dilution Compny GK15 1:2 ebioscience CD :2 ebioscience H1.2F3 1:2 ebioscience TCR H :2 ebioscience MHCI AF :2 ebioscience CD :2 ebioscience CD24 M1/69 1:2 ebioscience CD62L MEL-14 1:2 ebioscience 5.1 A2 1:2 BD Bioscience :2 BD Bioscience Foxp3 FJK-16s 1:2 ebioscience V :2 ebioscience Antiodies for Immunolot nlysis Antiody Code Dilution Compny nti-rit-ncor1 5948S 1:1 Cell Signling Technology nti-rit-bim 2933S 1:1 Cell Signling Technology nti-rit-p-plc S 1:1 Cell Signling Technology nti-mouse-plc :1 Acm nti-mouse-p- Erk1/2 sc :5 Snt Cruz Biotechnology nti-rit-erk sc-93 1:2 Snt Cruz Biotechnology nti-rit-p-p S 1:1 Cell Signling Technology nti-rit-p38 sc-728 1:2 Snt Cruz Biotechnology nti-rit- -ctin 497S 1:2 Cell Signling Technology nti-rit-tulin CP6 1:2 EMD Millipore Got nti-rit- IgG(H+L) :3 Jckson Immuno&Reserch Donkey ntimouse-igg(h+l) :3 Jckson Immuno&Reserch Antiodies for CHIP nlysis Antiody Code Dilution Compny nti-ncor1 5948S 1 g per IP Cell Signling Technology nti-h3c g per IP Millipore nti-h4c g per IP Millipore nti-h3k27c g per IP Acm nti-h3k4me g per IP Acm nti-h3k4me g per IP Acm IgG 39S 1 g per IP Cell Signling Technology

17 Supplementl Tle 3. Primer for Quntittive RT-PCR nlysis Ncor1 Forwrd 5'-TGCGTCAGCTTTCTGTGA TTCCACC-3' Reverse 5'-TGA TTTCTGCCTCTGCGTTTTCCA-3' Bim Forwrd 5'-CGACAGTCTCAGGAGGAACC-3' Reverse 5'-CCTTCTCCATACCAGACGGA-3' Fsl Forwrd 5'-TGAATTACCCATGTCCCCAG-3' Reverse 5'-AAACTGACCCTGGAGGAGCC-3' Tnf Forwrd 5'-CATCTTCTCAAAATTCGAGTGACAA-3' Reverse 5'-TGGGAGTAGACAAGGTACAACCC-3' Tril Forwrd 5'-ATGATGGTGATTTGCATAGTGCT-3' Reverse 5'-AGCTGCTTCATCTCGTTGGTG-3' Bk Forwrd 5'-AATGGCATCCGGACAAGGAC-3' Reverse 5'-TGTTCCTGCTGGTGGAGGTA-3' Act Forwrd 5'-GGCTGTATTCCCCTCCATCG-3' Reverse 5'-CCAGTTGGTAACAATGCCATGT-3'

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