Supplementary Table 1. Related to Figure 3. TCRtg101 differentially expressed genes. ,,,,,,,,,,,,,,,,,,,, ,gene,symbol,l2FC_early_vs_naive,p_adj_early_vs_naive,sig_early_vs_naive,l2FC_mid_vs_naive,p_adj_mid_vs_naive,sig_mid_vs_naive,l2FC_late_vs_naive,p_adj_late_vs_naive,sig_late_vs_naive,l2FC_mid_vs_early,p_adj_mid_vs_early,sig_mid_vs_early,l2FC_late_vs_early,p_adj_late_vs_early,sig_late_vs_early,l2FC_late_vs_mid,p_adj_late_vs_mid,sig_late_vs_mid 2,ENSMUSG00000000028.15,Cdc45,2.736978776,0.068216357,FALSE,4.711758972,2.18E-08,TRUE,4.930125441,1.17E-07,TRUE,1.974780196,0.268022604,FALSE,2.193146666,0.108816989,FALSE,0.218366469,1,FALSE 6,ENSMUSG00000000078.7,Klf6,-0.507287489,0.972399311,FALSE,-2.383893492,0.001347295,TRUE,-2.314875768,0.005240641,TRUE,-1.876606003,0.196473785,FALSE,-1.807588279,0.129967735,FALSE,0.069017724,1,FALSE 14,ENSMUSG00000000149.10,Gna12,-2.527074368,0.007983767,TRUE,0.112660636,0.90676677,FALSE,0.500810491,0.565099448,FALSE,2.639735003,0.00419744,TRUE,3.027884859,0.0011842,TRUE,0.388149856,1,FALSE 16,ENSMUSG00000000171.5,Sdhd,0.319071869,0.930827681,FALSE,0.91188877,0.012856308,TRUE,1.070575226,0.007979394,TRUE,0.592816901,0.497003517,FALSE,0.751503358,0.20638086,FALSE,0.158686456,1,FALSE 18,ENSMUSG00000000194.13,Gpr107,0.141293776,0.953430355,FALSE,0.44238519,0.011994017,TRUE,0.298580427,0.154119843,FALSE,0.301091414,0.452236322,FALSE,0.157286651,0.640710876,FALSE,-0.143804763,1,FALSE 23,ENSMUSG00000000278.10,Scpep1,0.243707192,0.965235238,FALSE,0.784328033,0.015127529,TRUE,0.907894537,0.010638119,TRUE,0.54062084,0.470981726,FALSE,0.664187344,0.200868633,FALSE,0.123566504,1,FALSE 25,ENSMUSG00000000290.13,Itgb2,0.561908774,0.411187906,FALSE,0.586049377,0.033797448,TRUE,0.553693906,0.076032263,FALSE,0.024140602,0.990465485,FALSE,-0.008214868,0.993248754,FALSE,-0.03235547,1,FALSE 26,ENSMUSG00000000295.13,Hddc2,0.257399624,0.94829627,FALSE,0.6698274,0.033011952,TRUE,1.173064203,0.000436311,TRUE,0.412427776,0.61133511,FALSE,0.915664579,0.048767993,TRUE,0.503236803,0.825453201,FALSE 27,ENSMUSG00000000303.12,Cdh1,3.674572454,0.375375111,FALSE,1.833431725,0.340833823,FALSE,-1.787547676,0.44289727,FALSE,-1.84114073,0.703177608,FALSE,-5.462120131,0.046906845,TRUE,-3.620979401,0.64325849,FALSE 28,ENSMUSG00000000317.11,Bcl6b,5.551919613,0.123252907,FALSE,6.350927582,0.002288738,TRUE,7.409579939,0.000621991,TRUE,0.799007968,0.900435127,FALSE,1.857660326,0.519248853,FALSE,1.058652357,1,FALSE 30,ENSMUSG00000000326.13,Comt,0.412969084,0.961006722,FALSE,0.947709994,0.084106084,FALSE,1.365577113,0.020197257,TRUE,0.53474091,0.734182995,FALSE,0.952608029,0.274685603,FALSE,0.417867119,1,FALSE 31,ENSMUSG00000000339.14,Rtca,0.078769627,1,FALSE,0.55519631,0.091475424,FALSE,0.950372965,0.006268289,TRUE,0.476426682,0.545491692,FALSE,0.871603337,0.071203124,FALSE,0.395176655,1,FALSE 41,ENSMUSG00000000409.14,Lck,-1.068900907,0.000154775,TRUE,-0.79731807,0.00027906,TRUE,-1.343382448,1.08E-08,TRUE,0.271582836,0.663793502,FALSE,-0.274481542,0.508842671,FALSE,-0.546064378,0.360900174,FALSE 44,ENSMUSG00000000440.12,Pparg,-7.111098591,0.228289061,FALSE,-0.581992097,0.866915697,FALSE,1.645900206,0.613594674,FALSE,6.529106493,0.270672037,FALSE,8.756998797,0.036668832,TRUE,2.227892304,1,FALSE 47,ENSMUSG00000000489.7,Pdgfb,4.021861303,0.066832075,FALSE,4.362453097,0.000834897,TRUE,4.483109848,0.001636708,TRUE,0.340591794,0.960202186,FALSE,0.461248544,0.87595971,FALSE,0.120656751,1,FALSE 50,ENSMUSG00000000532.11,Acvr1b,-0.611020796,0.857957171,FALSE,-1.943940411,0.000244784,TRUE,-1.946695527,0.001359602,TRUE,-1.332919615,0.203725595,FALSE,-1.33567473,0.127257645,FALSE,-0.002755115,1,FALSE 51,ENSMUSG00000000538.18,Tom1l2,1.461198959,0.810801249,FALSE,-1.405928509,0.273279374,FALSE,-3.232944194,0.021732306,TRUE,-2.867127468,0.200386749,FALSE,-4.694143152,0.00898405,TRUE,-1.827015684,0.930811654,FALSE 54,ENSMUSG00000000563.17,Atp5pb,0.27798955,0.961474554,FALSE,0.647538354,0.083703219,FALSE,0.856155923,0.03521931,TRUE,0.369548804,0.732521901,FALSE,0.578166373,0.34442364,FALSE,0.208617569,1,FALSE 57,ENSMUSG00000000581.8,C1d,0.15500254,0.994779086,FALSE,0.903896359,0.01543453,TRUE,1.31519832,0.00109238,TRUE,0.74889382,0.339229319,FALSE,1.16019578,0.035864632,TRUE,0.41130196,1,FALSE 58,ENSMUSG00000000594.7,Gm2a,-0.457398557,0.591454196,FALSE,0.40877583,0.155546722,FALSE,0.674836409,0.026667362,TRUE,0.866174387,0.044999812,TRUE,1.132234966,0.003207079,TRUE,0.266060579,1,FALSE 59,ENSMUSG00000000600.15,Krit1,0.223775846,0.990030916,FALSE,-0.069665493,0.914967011,FALSE,-1.226689464,0.016967156,TRUE,-0.293441339,0.85548947,FALSE,-1.45046531,0.034014593,TRUE,-1.157023972,0.312254141,FALSE 61,ENSMUSG00000000617.14,Grm6,1.789307095,0.876270425,FALSE,-0.48983587,0.834216829,FALSE,-5.644064564,0.028574561,TRUE,-2.279142965,0.60943681,FALSE,-7.433371659,0.018473626,TRUE,-5.154228694,0.460082694,FALSE 62,ENSMUSG00000000627.15,Sema4f,-0.286130575,0.982682933,FALSE,-1.658407924,0.001498397,TRUE,-1.429826439,0.015665628,TRUE,-1.372277349,0.167158164,FALSE,-1.143695864,0.182167297,FALSE,0.228581485,1,FALSE 63,ENSMUSG00000000628.10,Hk2,3.804398539,0.009312936,TRUE,4.436473252,5.62E-06,TRUE,4.173296268,0.000147045,TRUE,0.632074713,0.863914716,FALSE,0.368897729,0.874680081,FALSE,-0.263176984,1,FALSE 66,ENSMUSG00000000686.11,Abhd15,-0.179242275,1,FALSE,-2.520429688,0.00183555,TRUE,-1.994004579,0.030661083,TRUE,-2.341187413,0.104972616,FALSE,-1.814762304,0.168969142,FALSE,0.526425109,1,FALSE 69,ENSMUSG00000000732.9,Icosl,-0.708519512,0.953430355,FALSE,-2.4738131,0.005723257,TRUE,-2.317950296,0.024409378,TRUE,-1.765293588,0.360959937,FALSE,-1.609430784,0.291522434,FALSE,0.155862804,1,FALSE 77,ENSMUSG00000000782.15,Tcf7,-0.672300734,0.665996114,FALSE,-0.893892631,0.044240597,TRUE,-0.965311028,0.051055128,FALSE,-0.221591897,0.900988539,FALSE,-0.293010294,0.742938575,FALSE,-0.071418398,1,FALSE 78,ENSMUSG00000000787.12,Ddx3x,0.133218199,0.979701434,FALSE,-0.035947842,0.914643254,FALSE,-0.597969266,0.020743377,TRUE,-0.169166041,0.827249488,FALSE,-0.731187465,0.034584197,TRUE,-0.562021424,0.348091211,FALSE 79,ENSMUSG00000000804.14,Usp32,-0.599042617,0.54352067,FALSE,-1.008642733,0.002439391,TRUE,-1.461845987,7.63E-05,TRUE,-0.409600116,0.654595385,FALSE,-0.862803369,0.107963115,FALSE,-0.453203254,0.989849852,FALSE 81,ENSMUSG00000000817.10,Fasl,3.42875643,0.264566798,FALSE,4.576899412,0.001278946,TRUE,5.294905383,0.000663321,TRUE,1.148142982,0.805839988,FALSE,1.866148953,0.462057172,FALSE,0.718005971,1,FALSE 85,ENSMUSG00000000838.17,Fmr1,1.117736597,0.973734745,FALSE,3.640330531,0.046570278,TRUE,0.758112355,0.774381641,FALSE,2.522593934,0.578352161,FALSE,-0.359624242,0.936978267,FALSE,-2.882218177,0.867032495,FALSE 87,ENSMUSG00000000884.17,Gnb1l,0.843660718,0.857957171,FALSE,1.696837973,0.023120194,TRUE,1.450342077,0.086656324,FALSE,0.853177255,0.675722419,FALSE,0.606681359,0.670055099,FALSE,-0.246495896,1,FALSE 88,ENSMUSG00000000902.13,Smarcb1,0.715010253,0.835425508,FALSE,1.565963349,0.009151023,TRUE,1.876341254,0.004373081,TRUE,0.850953097,0.579709414,FALSE,1.161331001,0.239699729,FALSE,0.310377905,1,FALSE 89,ENSMUSG00000000915.15,Hip1r,0.160502087,0.984736559,FALSE,0.706505503,0.021555594,TRUE,1.151889344,0.000472779,TRUE,0.546003415,0.435539773,FALSE,0.991387257,0.028487988,TRUE,0.445383841,0.921217013,FALSE 91,ENSMUSG00000000934.9,Top1mt,1.033158151,0.243166184,FALSE,1.258518676,0.002835098,TRUE,0.792828342,0.107477675,FALSE,0.225360525,0.892530005,FALSE,-0.240329809,0.786402863,FALSE,-0.465690335,1,FALSE 97,ENSMUSG00000000982.5,Ccl3,7.967784463,1.70E-05,TRUE,7.984758582,1.26E-08,TRUE,7.251252025,4.71E-06,TRUE,0.01697412,1,FALSE,-0.716532438,0.823058993,FALSE,-0.733506557,1,FALSE 99,ENSMUSG00000001016.12,Ilf2,0.396973332,0.803187574,FALSE,0.581367497,0.06667893,FALSE,0.775973265,0.024298098,TRUE,0.184394165,0.871860231,FALSE,0.378999933,0.494643596,FALSE,0.194605767,1,FALSE 100,ENSMUSG00000001018.15,Snapin,-1.185099772,0.696706797,FALSE,-0.516558804,0.58985747,FALSE,-1.984506764,0.031734956,TRUE,0.668540968,0.795736812,FALSE,-0.799406992,0.604299702,FALSE,-1.46794796,0.749180131,FALSE 101,ENSMUSG00000001020.8,S100a4,2.587173197,0.296371411,FALSE,5.68261149,6.48E-08,TRUE,6.23374566,9.03E-08,TRUE,3.095438294,0.114640327,FALSE,3.646572463,0.026585694,TRUE,0.551134169,1,FALSE 102,ENSMUSG00000001025.8,S100a6,2.077150846,0.307087912,FALSE,3.773393346,1.60E-05,TRUE,3.56916132,0.000280234,TRUE,1.6962425,0.396598641,FALSE,1.492010475,0.329237027,FALSE,-0.204232026,1,FALSE 108,ENSMUSG00000001054.9,Rmnd5b,0.460499666,0.995633156,FALSE,-1.271155573,0.34735114,FALSE,-3.083748814,0.02711237,TRUE,-1.73165524,0.574768636,FALSE,-3.54424848,0.061700826,FALSE,-1.812593241,0.92951229,FALSE 109,ENSMUSG00000001056.3,Nhp2,1.305327073,0.422638765,FALSE,1.664852129,0.009172767,TRUE,1.675604761,0.018733526,TRUE,0.359525057,0.883973108,FALSE,0.370277688,0.782552102,FALSE,0.010752631,1,FALSE 111,ENSMUSG00000001065.15,Zfp276,-0.630972986,0.448683464,FALSE,-1.046582491,0.000883517,TRUE,-1.85905332,6.06E-08,TRUE,-0.415609505,0.629646607,FALSE,-1.228080334,0.008732404,TRUE,-0.812470829,0.332060045,FALSE 112,ENSMUSG00000001082.12,Mfsd10,2.065908416,0.414239342,FALSE,2.300343845,0.023037579,TRUE,3.124461371,0.004211787,TRUE,0.234435429,0.965417745,FALSE,1.058552956,0.561888212,FALSE,0.824117527,1,FALSE 115,ENSMUSG00000001100.10,Poldip2,0.454472344,0.858135439,FALSE,0.9246035,0.023504764,TRUE,0.922111178,0.043864819,TRUE,0.470131156,0.67887041,FALSE,0.467638834,0.526684352,FALSE,-0.002492322,1,FALSE 116,ENSMUSG00000001105.15,Ift20,-0.070471999,1,FALSE,0.913953932,0.039500509,TRUE,0.880149169,0.078775846,FALSE,0.984425931,0.267988098,FALSE,0.950621167,0.175058872,FALSE,-0.033804764,1,FALSE 118,ENSMUSG00000001123.15,Lgals9,0.080996194,0.989859197,FALSE,0.348456276,0.033123946,TRUE,0.439438374,0.014248988,TRUE,0.267460082,0.480096085,FALSE,0.358442179,0.166204909,FALSE,0.090982098,1,FALSE 119,ENSMUSG00000001127.12,Araf,-1.441679278,0.627423672,FALSE,-2.646162974,0.003066084,TRUE,-1.286424501,0.229872802,FALSE,-1.204483696,0.616333486,FALSE,0.155254777,0.946234481,FALSE,1.359738473,0.913388478,FALSE 120,ENSMUSG00000001128.7,Cfp,-3.829500269,0.032269857,TRUE,-4.337725641,0.000108889,TRUE,-4.048291234,0.001454409,TRUE,-0.508225372,0.920182431,FALSE,-0.218790965,0.94232213,FALSE,0.289434407,1,FALSE 125,ENSMUSG00000001156.9,Mxd1,-0.372968425,0.874804036,FALSE,-0.764250479,0.032950027,TRUE,-0.835928741,0.037647444,TRUE,-0.391282054,0.70098253,FALSE,-0.462960316,0.465907456,FALSE,-0.071678262,1,FALSE 127,ENSMUSG00000001158.13,Snrnp27,0.016000947,1,FALSE,0.684602821,0.027874513,TRUE,0.941987592,0.005278318,TRUE,0.668601874,0.292318078,FALSE,0.925986644,0.045484859,TRUE,0.257384771,1,FALSE 129,ENSMUSG00000001173.15,Ocrl,-0.522756703,0.869931167,FALSE,-1.06130028,0.031891535,TRUE,-1.059920355,0.064027107,FALSE,-0.538543577,0.697027927,FALSE,-0.537163652,0.555834268,FALSE,0.001379925,1,FALSE 130,ENSMUSG00000001175.15,Calm1,-0.114242695,0.990030916,FALSE,0.519654912,0.03391365,TRUE,0.6035749,0.025728189,TRUE,0.633897607,0.158084216,FALSE,0.717817594,0.0497753,TRUE,0.083919988,1,FALSE 133,ENSMUSG00000001228.14,Uhrf1,3.285848201,0.093186502,FALSE,4.271506021,0.000102695,TRUE,4.464976276,0.000254153,TRUE,0.98565782,0.783504436,FALSE,1.179128075,0.574017138,FALSE,0.193470255,1,FALSE 142,ENSMUSG00000001289.12,Pfdn5,-0.671054911,0.54153054,FALSE,0.481670975,0.217431692,FALSE,1.485955828,0.000108629,TRUE,1.152725887,0.046535796,TRUE,2.15701074,3.70E-06,TRUE,1.004284853,0.133666508,FALSE 144,ENSMUSG00000001305.5,Rrp15,1.015920407,0.268926727,FALSE,1.299642289,0.002242017,TRUE,0.976444199,0.044707972,TRUE,0.283721882,0.8543774,FALSE,-0.039476209,0.974766,FALSE,-0.323198091,1,FALSE 148,ENSMUSG00000001348.15,Acp5,-0.807345714,0.699257731,FALSE,-1.02138395,0.068869648,FALSE,-1.702450691,0.004426064,TRUE,-0.214038236,0.929657081,FALSE,-0.895104977,0.331292362,FALSE,-0.681066741,1,FALSE 151,ENSMUSG00000001380.7,Hars,0.575922335,0.615829452,FALSE,1.044770897,0.002700222,TRUE,1.018265008,0.008705931,TRUE,0.468848562,0.614395945,FALSE,0.442342673,0.484552412,FALSE,-0.026505889,1,FALSE 152,ENSMUSG00000001383.9,Zmat2,0.113827841,0.990030916,FALSE,0.477525954,0.040846377,TRUE,0.564746599,0.028292621,TRUE,0.363698112,0.507132274,FALSE,0.450918757,0.229196425,FALSE,0.087220645,1,FALSE 153,ENSMUSG00000001403.13,Ube2c,1.870294518,0.508959995,FALSE,4.492226927,2.38E-06,TRUE,5.316012276,4.18E-07,TRUE,2.621932408,0.156208616,FALSE,3.445717757,0.018174072,TRUE,0.823785349,1,FALSE 155,ENSMUSG00000001416.13,Cct3,0.747313538,0.689377806,FALSE,1.019389746,0.045005445,TRUE,1.068063368,0.060283182,FALSE,0.272076208,0.889509337,FALSE,0.32074983,0.75530307,FALSE,0.048673622,1,FALSE 157,ENSMUSG00000001419.17,Mef2d,-0.308565223,0.939521956,FALSE,-0.781922273,0.035066223,TRUE,-1.116911881,0.005705956,TRUE,-0.473357051,0.632264147,FALSE,-0.808346659,0.171106021,FALSE,-0.334989608,1,FALSE 160,ENSMUSG00000001440.5,Kpnb1,0.318163964,0.923177833,FALSE,0.800457726,0.024615897,TRUE,0.636142332,0.119477967,FALSE,0.482293761,0.603203231,FALSE,0.317978368,0.638183025,FALSE,-0.164315394,1,FALSE 161,ENSMUSG00000001444.2,Tbx21,2.930743085,0.027097355,TRUE,4.281088396,1.45E-07,TRUE,3.771049172,4.80E-05,TRUE,1.35034531,0.523882722,FALSE,0.840306086,0.60732178,FALSE,-0.510039224,1,FALSE 162,ENSMUSG00000001445.10,Mrpl10,0.39392778,0.684227307,FALSE,0.832407662,0.001165696,TRUE,0.942481858,0.000829963,TRUE,0.438479881,0.47296449,FALSE,0.548554077,0.192199881,FALSE,0.110074196,1,FALSE 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