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. 2020 Sep 22;11(5):e01911-20. doi: 10.1128/mBio.01911-20

TABLE 2.

List of differentially regulated stem cell related genes in early organoids versus late organoids

Probe Gene symbol RefSeq Entrez ID logFC Avg expression t score P
A_23_P374844 GAL NM_015973 51083 5.55 9.38 23.45 0.00
A_24_P225616 RRM2 NM_001034 6241 4.23 9.90 26.43 0.00
A_24_P397107 CDC25A NM_001789 993 3.39 10.26 23.07 0.00
A_32_P194264 CHAC2 NM_001008708 494143 2.75 10.21 9.17 0.01
A_33_P3286208 LRR1 NM_203467 122769 2.61 8.83 20.53 0.00
A_33_P3332126 SCLY ENST00000409736 51540 2.45 9.74 17.13 0.00
A_33_P3387856 CENPN NM_001100625 55839 2.42 6.42 6.88 0.01
A_23_P88740 CENPN NM_018455 55839 2.22 12.96 12.74 0.00
A_24_P83678 MMS22L NM_198468 253714 2.14 8.86 8.09 0.01
A_23_P325040 TMPO NM_003276 7112 2.14 8.95 13.02 0.00
A_23_P56553 METTL8 NM_024770 79828 2.07 10.98 12.13 0.00
A_33_P3253707 LRR1 NM_152329 122769 2.06 12.60 14.00 0.00
A_33_P3379886 FGF2 NM_002006 2247 1.99 6.35 3.18 0.07
A_23_P217637 TIMM8A NM_004085 1678 1.94 11.61 11.10 0.00
A_33_P3419696 FGF2 NM_002006 2247 1.92 7.69 4.99 0.03
A_24_P49747 HMGB3P24 ENST00000433260 NAa 1.89 6.61 15.70 0.00
A_33_P3489737 NLN NM_020726 57486 1.86 10.59 5.83 0.02
A_24_P244699 NUDT15 NM_018283 55270 1.81 9.55 6.06 0.02
A_24_P178093 TOMM40 NM_006114 10452 1.77 8.62 10.80 0.00
A_32_P95914 MMS22L NM_198468 253714 1.75 9.70 6.71 0.01
A_23_P143958 RPL22L1 NM_001099645 200916 1.66 16.39 8.91 0.01
A_24_P336853 PNO1 NM_020143 56902 1.61 10.31 12.46 0.00
A_33_P3357082 METTL8 NM_024770 79828 1.59 9.10 13.84 0.00
A_23_P82823 PINX1 NM_017884 54984 1.57 10.41 10.49 0.00
A_23_P209337 METTL21A NM_145280 151194 1.56 10.87 6.70 0.01
A_33_P3250861 ZIC3 ENST00000370606 7547 1.29 4.62 1.57 0.24
A_23_P144337 CCRN4L NM_012118 25819 1.29 3.26 6.09 0.02
A_32_P25273 HSPD1 NM_002156 3329 1.24 17.11 11.51 0.00
A_23_P150092 SEPHS1 NM_012247 22929 1.21 12.66 7.32 0.01
A_21_P0000006 TOMM40 NM_001128917 10452 1.21 13.86 9.57 0.01
A_33_P3412613 TMPO NM_001032283 7112 1.18 5.82 6.27 0.02
A_23_P202143 NOLC1 NM_004741 9221 1.13 12.02 4.96 0.03
A_33_P3619171 PMAIP1 NM_021127 5366 1.09 10.98 4.95 0.03
A_24_P253215 EMG1 NM_006331 10436 1.07 12.98 6.16 0.02
A_32_P71788 FKBP4 NM_002014 2288 1.06 8.96 9.26 0.01
A_24_P357266 GRPR NM_005314 2925 1.01 4.42 1.66 0.22
A_23_P136504 SLC25A21 NM_030631 89874 1.01 5.54 3.14 0.07
A_24_P297888 MTAP NM_002451 4507 1.00 9.97 7.12 0.01
A_33_P3256425 BICD1 NM_001714 636 0.94 6.25 2.98 0.08
A_23_P345065 SCLY NM_016510 51540 0.93 10.96 3.47 0.06
A_23_P160881 SMPDL3B NM_001009568 27293 0.93 9.95 2.62 0.10
A_23_P27167 RNASEH1 NM_002936 246243 0.93 11.31 5.67 0.02
A_23_P365060 MDN1 NM_014611 23195 0.92 6.39 7.63 0.01
A_33_P3388135 MKKS NM_170784 8195 0.92 13.58 3.97 0.04
A_23_P164141 PSME3 NM_176863 10197 0.89 10.79 7.38 0.01
A_23_P156842 EEF1E1 NM_004280 9521 0.89 13.42 7.96 0.01
A_33_P3287815 DDX21 NM_004728 9188 0.87 13.48 8.11 0.01
A_23_P43726 NUP160 NM_015231 23279 0.86 11.39 6.96 0.01
A_21_P0011842 EEF1E1 NM_001135650 9521 0.86 13.35 5.47 0.02
A_23_P131954 SNX5 NM_014426 27131 0.86 15.01 4.18 0.04
A_23_P148484 RLIM NM_016120 51132 0.86 10.97 3.37 0.06
A_23_P252362 MRPS30 NM_016640 10884 0.86 10.49 6.46 0.01
A_24_P134727 TFAM NM_003201 7019 0.83 9.21 7.42 0.01
A_23_P214907 MTHFD1L NM_015440 25902 0.82 9.75 2.11 0.15
A_23_P256148 AKIRIN1 NM_024595 79647 0.81 11.04 3.58 0.05
A_33_P3287502 MSH2 NM_000251 4436 0.77 11.49 5.50 0.02
A_23_P128991 SLIRP NM_031210 81892 0.77 14.35 2.63 0.10
A_33_P3285444 TERF1 NM_017489 7013 0.76 4.75 1.48 0.26
A_24_P50458 TERF1 NM_017489 7013 0.76 12.20 3.75 0.05
A_33_P3242659 KIF13A NM_022113 63971 0.70 5.56 3.56 0.05
A_33_P3329108 MTAP NM_002451 4507 0.69 11.71 3.99 0.04
A_23_P333951 DNAH14 NM_144989 127602 0.67 9.74 2.67 0.10
A_23_P137484 L1TD1 NM_019079 54596 0.67 5.12 5.21 0.02
A_23_P128372 FKBP4 NM_002014 2288 0.65 12.78 4.38 0.04
A_33_P3294404 AKIRIN1 NM_024595 79647 0.64 10.32 3.56 0.05
A_23_P216149 TERF1 NM_017489 7013 0.64 11.57 1.77 0.20
A_23_P102471 MSH2 NM_000251 4436 0.59 12.22 5.40 0.02
A_24_P854913 METTL21A NM_001127395 151194 0.56 11.08 1.39 0.28
A_23_P54540 EIF2AK4 NM_001013703 440275 0.55 11.76 3.94 0.04
A_23_P94636 RC3H2 NM_018835 54542 0.49 9.40 4.46 0.03
A_23_P146997 TXLNG NM_018360 55787 0.48 9.65 1.61 0.23
A_33_P3389188 TFAM NM_003201 7019 0.47 12.74 1.88 0.18
A_33_P3354267 AKIRIN1 NM_024595 79647 0.47 11.81 3.21 0.07
A_33_P3283906 NIP7 NM_016101 51388 0.46 12.12 3.33 0.06
A_33_P3345504 RC3H2 NM_018835 54542 0.45 7.47 4.19 0.04
A_33_P3299776 NODAL NM_018055 4838 0.45 3.81 1.54 0.25
A_32_P220696 TERF1 NM_017489 7013 0.45 10.55 1.81 0.19
A_23_P213908 PHAX NM_032177 51808 0.44 13.19 3.43 0.06
A_24_P192434 TERF1 NM_017489 7013 0.44 10.44 1.56 0.24
A_33_P3241786 ADD2 NM_017482 119 0.40 3.31 1.34 0.29
A_32_P87531 DNAH14 NM_001145154 127602 0.35 8.81 1.17 0.35
A_33_P3269453 BPTF ENST00000342579 2186 0.34 10.51 1.74 0.20
A_21_P0000013 TIMM8A NM_001145951 1678 0.34 10.14 2.88 0.08
A_33_P3278118 CASP3 NM_004346 836 0.32 8.43 0.86 0.47
A_23_P134008 USP45 ENST00000472914 85015 0.31 9.59 1.34 0.29
A_33_P3297978 MYO1E NM_004998 4643 0.30 14.27 2.24 0.13
A_24_P127691 DNAH14 ENST00000495456 127602 0.29 4.94 1.91 0.18
A_33_P3289996 USP45 NM_001080481 85015 0.27 7.74 2.52 0.11
A_24_P281975 GNPTAB NM_024312 79158 0.25 11.60 1.16 0.35
A_24_P215407 DDX6 NM_004397 1656 0.25 8.91 2.20 0.14
A_33_P3289995 USP45 ENST00000369232 85015 0.24 4.91 2.23 0.14
A_33_P3409506 C9orf85 NM_182505 138241 0.20 8.88 1.66 0.22
A_32_P104478 FGD6 NM_018351 55785 0.17 11.00 0.86 0.47
A_33_P3418294 DNAH14 NM_001373 127602 0.15 3.15 1.24 0.32
A_24_P51118 MTAP NM_002451 4507 0.14 10.15 0.28 0.80
A_23_P214354 EXOC2 NM_018303 55770 0.11 8.27 0.33 0.77
A_33_P3235340 DDX18 NM_006773 8886 0.11 13.07 0.98 0.42
A_33_P3269976 GAL ENST00000538401 51083 0.10 2.93 0.84 0.48
A_23_P86504 C10orf76 NM_024541 79591 0.10 11.60 0.74 0.53
A_33_P3291976 TERF1 ENST00000518695 7013 0.07 5.35 0.46 0.69
A_23_P92410 CASP3 NM_004346 836 0.06 14.49 0.52 0.65
A_32_P44775 C9orf85 NM_182505 138241 0.05 9.97 0.38 0.73
A_33_P3414669 RLIM NM_183353 51132 0.04 6.26 0.40 0.72
A_23_P351215 SKIL NM_005414 6498 0.04 7.47 0.34 0.76
A_24_P152404 C10orf76 ENST00000311122 79591 0.03 10.23 0.16 0.89
A_32_P135243 MTHFD1L NM_015440 25902 0.03 10.60 0.11 0.92
A_32_P80255 DDX6 NM_004397 1656 0.03 10.53 0.15 0.89
A_32_P528967 RTP1 NM_153708 132112 0.02 3.05 0.18 0.87
A_21_P0013574 MTHFD1L NM_001242767 25902 0.02 11.20 0.10 0.93
A_33_P3378972 UNC5D NM_080872 137970 0.01 3.02 0.12 0.92
A_32_P741851 GLB1L3 NM_001080407 112937 0.01 2.96 0.11 0.92
A_23_P140362 VRTN NM_018228 55237 0.01 2.86 0.11 0.92
A_33_P3241782 ADD2 NM_001617 119 0.01 2.76 0.08 0.94
A_23_P72817 GDF3 NM_020634 9573 0.01 2.91 0.05 0.96
A_23_P329798 CER1 NM_005454 9350 0.00 2.67 0.04 0.97
A_23_P5370 RPRM NM_019845 56475 0.00 2.84 0.03 0.98
A_23_P327910 ZIC3 NM_003413 7547 0.00 2.83 0.03 0.98
A_33_P3419632 GLB1L3 ENST00000389887 112937 0.00 3.57 0.01 1.00
A_23_P216118 UNC5D NM_080872 137970 0.00 2.95 0.02 0.99
A_21_P0014207 LOC100506507 XR_108853 NA 0.00 2.66 0.01 0.99
A_23_P380526 DPPA4 NM_018189 55211 0.00 2.81 −0.04 0.97
A_23_P421436 ADD2 NM_017488 119 −0.01 2.84 −0.05 0.96
A_19_P00318232 SHISA9 NM_001145205 729993 −0.01 2.81 −0.06 0.96
A_33_P3280729 SHISA9 NM_001145204 729993 −0.01 2.88 −0.06 0.96
A_23_P137573 LEFTY2 NM_003240 7044 −0.01 2.87 −0.06 0.96
A_24_P235049 MTHFD1L NM_015440 25902 −0.02 11.42 −0.10 0.93
A_32_P213091 SHISA9 NM_001145205 729993 −0.03 4.56 −0.26 0.82
A_23_P375147 RC3H2 ENST00000373670 54542 −0.05 11.16 −0.18 0.87
A_24_P380132 G3BP2 NM_203505 9908 −0.06 14.44 −0.28 0.80
A_23_P70168 TARS NM_152295 6897 −0.11 14.69 −0.58 0.61
A_23_P79962 MKKS NM_170784 8195 −0.11 12.65 −0.85 0.47
A_23_P84070 LARP7 NM_016648 51574 −0.11 12.56 −0.98 0.42
A_33_P3297245 RRAS2 NM_012250 22800 −0.12 14.04 −1.06 0.38
A_24_P332230 LARP7 NM_016648 51574 −0.12 13.09 −0.72 0.54
A_24_P943922 CACHD1 NM_020925 57685 −0.14 4.65 −0.18 0.87
A_33_P3307775 DENR NM_003677 8562 −0.14 7.10 −0.44 0.69
A_33_P3862375 USP45 NM_001080481 85015 −0.14 9.20 −0.32 0.78
A_33_P3234317 RRAS2 NM_012250 22800 −0.15 13.91 −1.31 0.30
A_33_P3378644 PHC1 NM_004426 1911 −0.19 7.01 −1.11 0.37
A_23_P47058 CUZD1 NM_022034 50624 −0.22 8.19 −1.04 0.39
A_23_P215484 CCL26 NM_006072 10344 −0.26 4.06 −1.35 0.29
A_23_P427217 JMJD1C NM_032776 221037 −0.46 9.97 −3.89 0.05
A_23_P346265 GNPTAB NM_024312 79158 −0.47 9.02 −1.41 0.28
A_24_P940125 CNOT6 NM_015455 57472 −0.50 11.75 −4.61 0.03
A_33_P3295523 RAC3 NM_005052 5881 −0.50 12.37 −3.43 0.06
A_23_P25587 LECT1 NM_007015 11061 −0.51 4.69 −1.91 0.18
A_24_P347624 SNURF NM_022804 8926 −0.52 13.32 −1.90 0.18
A_23_P204246 PHC1 NM_004426 1911 −0.55 4.48 −0.98 0.42
A_23_P259127 ESRP1 NM_017697 54845 −0.60 11.38 −1.91 0.18
A_23_P366376 TDGF1 NM_003212 6997 −0.65 7.90 −2.86 0.08
A_24_P144601 POU5F1 NM_002701 5460 −0.66 7.98 −2.07 0.15
A_23_P156809 METTL21A NM_001127395 151194 −0.66 11.71 −5.71 0.02
A_24_P104538 BPTF ENST00000342579 2186 −0.67 9.15 −2.77 0.09
A_21_P0000084 SLC25A21 NM_030631 89874 −0.68 3.26 −1.42 0.27
A_23_P72770 USP44 NM_032147 84101 −0.79 7.71 −7.30 0.01
A_33_P3309206 GABRB3 ENST00000556166 2562 −0.87 4.56 −7.79 0.01
A_23_P59138 POU5F1 NM_002701 5460 −0.99 12.96 −6.27 0.02
A_33_P3227506 BPTF NM_182641 2186 −1.01 9.64 −6.30 0.02
A_33_P3277075 GABRB3 NM_000814 2562 −1.04 8.28 −9.63 0.01
A_24_P52921 BCAT1 NM_005504 586 −1.06 3.48 −4.10 0.04
A_24_P314477 TUBB2B NM_178012 347733 −1.14 7.23 −10.24 0.01
A_23_P323094 PHC1 NM_004426 1911 −1.24 6.06 −4.36 0.04
A_33_P3242014 PHC1 NM_004426 1911 −1.26 10.65 −9.28 0.01
A_23_P204640 NANOG NM_024865 79923 −1.66 7.94 −7.10 0.01
A_24_P935986 BCAT1 NM_005504 586 −1.77 9.14 −9.18 0.01
A_23_P160336 LEFTY1 NM_020997 10637 −2.93 4.40 −21.49 0.00
a

NA, not applicable.