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Differentially expressed genes in the pluripotent state

6. Appendix

6.1 Differentially expressed genes in the pluripotent state

Genes upregulated in dnmt1-/- ESCs compared to wt ESCs Gene symbol Entrez

Gene ID Fold change

to wt ESCs Gene name

1700013H16Rik 75514 1.67 RIKEN cDNA 1700013H16 gene AV320801 331531 2.85 expressed sequence AV320801 Dazl 13164 2.01 deleted in azoospermia-like Dcdc2a 195208 1.34 doublecortin domain containing 2a

Dnajc5g 231098 1.36 DnaJ (Hsp40) homolog, subfamily C, member 5 gamma Efhc2 74405 3.44 EF-hand domain (C-terminal) containing 2

Fkbp6 94244 1.81 FK506 binding protein 6 Fthl17 83457 1.65 ferritin, heavy polypeptide-like 17 Gm13154 433804 1.21 predicted gene 13154

Gm13498 227885 1.83 predicted gene 13498

Gm2889 10004065

8 2.1

hypothetical protein LOC100041609; hypothetical protein LOC100044795; predicted gene 3395;

similar to gag polyprotein; hypothetical protein LOC100047557; hypothetical protein LOC100040347; hypothetical protein LOC100044384; hypothetical protein LOC100045342;

hypothetical protein LOC100038979; predicted gene 2889

Gm4638 10004377

5 2.78 predicted gene 4638

Gm5128 331529 3.08 predicted gene 7903; predicted gene 5128 Gm5635 434729 1.18 predicted gene 5635

Gpat2 215456 1.45 RIKEN cDNA A530057A03 gene

Gpx6 75512 1.23 glutathione peroxidase 6

Gtsf1 74174 1.67 gametocyte specific factor 1

Hormad1 67981 2.42 HORMA domain containing 1; predicted gene 7167 Kdm5d 20592 1.04 lysine (K)-specific demethylase 5D

LOC280487 280487 2.78 pol polyprotein

Magea1 17137 1.42 melanoma antigen, family A, 1 Nckap1l 105855 1.54 NCK associated protein 1 like Nlrc4 268973 1.48 NLR family, CARD domain containing 4 Nlrp4c 83564 1.61 NLR family, pyrin domain containing 4C Nxf3 245610 1.72 nuclear RNA export factor 3

Olfr307 258610 2.51 olfactory receptor 307 Pnma5 385377 1.58 paraneoplastic antigen family 5

Pramel3 83565 2.96 preferentially expressed antigen in melanoma-like 3

Rbmy1a1 19657 1.58 RNA binding motif protein, Y chromosome, family 1, member A1 Rnf17 30054 1.28 ring finger protein 17

Rpl39l 68172 2.41 ribosomal protein L39-like

Scml2 107815 1.64 similar to sex comb on midleg-like 2 (Drosophila); sex comb on midleg-like 2 (Drosophila) Serpina3m 20717 1.45 serine (or cysteine) peptidase inhibitor, clade A, member 3M

Slc5a4b 64454 1.92 solute carrier family 5 (neutral amino acid transporters, system A), member 4b Smc1b 140557 2.27 structural maintenance of chromosomes 1B

Sohlh2 74434 1.4 spermatogenesis and oogenesis specific basic helix-loop-helix 2 Stk31 77485 1.69 serine threonine kinase 31

Ube1y1 22202 1.35 similar to ubiquitin activating enzyme E1; ubiquitin-activating enzyme E1, Chr Y 1 Usp9y 107868 1.39 ubiquitin specific peptidase 9, Y chromosome

Vmn2r-ps104 10004191

5 1.05 vomeronasal 2, receptor, pseudogene 104 Wfdc15a 68221 1.85 WAP four-disulfide core domain 15A

Xlr3a 22445 3.35

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked lymphocyte-lymphocyte-regulated 3A; X-linked lymphocyte-lymphocyte-regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr3b 574437 3.48

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked lymphocyte-lymphocyte-regulated 3A; X-linked lymphocyte-lymphocyte-regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

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Xlr3c 22446 3.54

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked lymphocyte-lymphocyte-regulated 3A; X-linked lymphocyte-lymphocyte-regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr4b 27083 3.07 X-linked lymphocyte-regulated 4D; X-linked lymphocyte-regulated 4E, pseudogene; X-linked lymphocyte-regulated 4B; X-linked lymphocyte-regulated 4C; hypothetical protein LOC100044049

Xlr4c 72891 3.36

X-linked lymphocyte-regulated 4D; X-linked lymphocyte-regulated 4E, pseudogene; X-linked lymphocyte-regulated 4B; X-linked lymphocyte-regulated 4C; hypothetical protein LOC100044049

Xlr5a 574438 4.48

X-linked lymphocyte-regulated 5B; X-linked lymphocyte-regulated 5D, pseudogene; X-linked lymphocyte-regulated 5A; X-linked lymphocyte-regulated 5E, pseudogene; predicted gene, EG667719

Xlr5b 627081 5.05

X-linked lymphocyte-regulated 5B; X-linked lymphocyte-regulated 5D, pseudogene; X-linked lymphocyte-regulated 5A; X-linked lymphocyte-regulated 5E, pseudogene; predicted gene, EG667719

Zfy1 22767 1.94 zinc finger protein 1, Y linked

Genes down regulated in dnmt1-/- ESCs compared to wt ESCs Gene symbol Entrez

Gene ID Fold change

to wt ESCs Gene name

Dnmt1 13433 -1.02 DNA methyltransferase (cytosine-5) 1

Eif4g3 230861 -1.03 eukaryotic translation initiation factor 4 gamma, 3; similar to Eukaryotic translation initiation factor 4 gamma 3 (eIF-4-gamma 3) (eIF-4G 3) (eIF4G 3) (eIF-4-gamma II) (eIF4GII)

Frmd4b 232288 -1.13 FERM domain containing 4B

Lphn2 99633 -1.53 latrophilin 2

Sema6a 20358 -2.12 sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A

Genes upregulated in TKO ESCs compared to wt ESCs Gene symbol Entrez

Gene ID Fold change

to wt ESCs Gene name

1700013H16Rik 75514 1.81 RIKEN cDNA 1700013H16 gene 1700080O16Rik 74279 1.14 RIKEN cDNA 1700080O16 gene 4930591A17Rik 68175 1.51 RIKEN cDNA 4930591A17 gene 9030617O03Rik 217830 1.04 RIKEN cDNA 9030617O03 gene

Asz1 74068 1.49 ankyrin repeat, SAM and basic leucine zipper domain containing 1 AV320801 331531 3.61 expressed sequence AV320801

Camk1d 227541 1.14 calcium/calmodulin-dependent protein kinase ID Ctcfl 664799 1.99 CCCTC-binding factor (zinc finger protein)-like Dazl 13164 2.39 deleted in azoospermia-like

Dcdc2a 195208 1.52 doublecortin domain containing 2a

Dnajc5g 231098 1.71 DnaJ (Hsp40) homolog, subfamily C, member 5 gamma Efhc2 74405 3.58 EF-hand domain (C-terminal) containing 2

Fkbp6 94244 2.16 FK506 binding protein 6 Fthl17 83457 1.5 ferritin, heavy polypeptide-like 17 Gm13498 227885 2.38 predicted gene 13498

Gm2889 1000406

58 2.35

hypothetical protein LOC100041609; hypothetical protein LOC100044795; predicted gene 3395;

similar to gag polyprotein; hypothetical protein LOC100047557; hypothetical protein LOC100040347; hypothetical protein LOC100044384; hypothetical protein LOC100045342;

hypothetical protein LOC100038979; predicted gene 2889 Gm5128 331529 3.91 predicted gene 7903; predicted gene 5128

Gpa33 59290 1.15 glycoprotein A33 (transmembrane)

Gpat2 215456 1.34 RIKEN cDNA A530057A03 gene

Gpx6 75512 1.43 glutathione peroxidase 6

Gtsf1 74174 1.59 gametocyte specific factor 1

Hormad1 67981 2.71 HORMA domain containing 1; predicted gene 7167 Magea1 17137 2.42 melanoma antigen, family A, 1

Magea2 17138 2.01 melanoma antigen, family A, 2 Magea4 17140 1.86 melanoma antigen, family A, 4 Magea5 17141 1.87 melanoma antigen, family A, 5 Magea6 17142 1.58 melanoma antigen, family A, 6 Mov10l1 83456 1.46 Moloney leukemia virus 10-like 1 Nckap1l 105855 1.75 NCK associated protein 1 like Nlrp4c 83564 1.58 NLR family, pyrin domain containing 4C Nxf3 245610 1.61 nuclear RNA export factor 3

Olfr307 258610 2.17 olfactory receptor 307

Pde8a 18584 1.13 phosphodiesterase 8A; similar to cAMP-specific cyclic nucleotide phosphodiesterase PDE8;

MMPDE8

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Piwil2 57746 1.3 piwi-like homolog 2 (Drosophila) Pnma5 385377 1.62 paraneoplastic antigen family 5

Ppp3ca 19055 1.05 protein phosphatase 3, catalytic subunit, alpha isoform Pramel3 83565 3.75 preferentially expressed antigen in melanoma-like 3 Rhox13 73614 1.25 reproductive homeobox 13

Rhox2a 75199 1.27 reproductive homeobox 2C; reproductive homeobox 2B; reproductive homeobox 2A; reproductive homeobox 2E

Rhox2e 1000400

16 1.26 reproductive homeobox 2C; reproductive homeobox 2B; reproductive homeobox 2A; reproductive homeobox 2E

Rnf17 30054 1.06 ring finger protein 17

Scml2 107815 2.16 similar to sex comb on midleg-like 2 (Drosophila); sex comb on midleg-like 2 (Drosophila) Smc1b 140557 2.47 structural maintenance of chromosomes 1B

Snx25 102141 1.42 sorting nexin 25

Sohlh2 74434 1.53 spermatogenesis and oogenesis specific basic helix-loop-helix 2 Spink10 328971 1.12 serine peptidase inhibitor, Kazal type 10

Stra8 20899 1.12 stimulated by retinoic acid gene 8

Taf9b 407786 1.46 TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor Tuba3b 22147 1.55 predicted gene 5366; tubulin, alpha 3B; tubulin, alpha 3A

Wfdc15a 68221 1.82 WAP four-disulfide core domain 15A

Xlr3a 22445 3.16

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked lymphocyte-lymphocyte-regulated 3A; X-linked lymphocyte-lymphocyte-regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr3b 574437 3.32

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked lymphocyte-lymphocyte-regulated 3A; X-linked lymphocyte-lymphocyte-regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr3c 22446 3.36

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked lymphocyte-lymphocyte-regulated 3A; X-linked lymphocyte-lymphocyte-regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr4b 27083 3.09 X-linked lymphocyte-regulated 4D; X-linked lymphocyte-regulated 4E, pseudogene; X-linked lymphocyte-regulated 4B; X-linked lymphocyte-regulated 4C; hypothetical protein LOC100044049 Xlr4c 72891 3.34 X-linked lymphocyte-regulated 4D; X-linked lymphocyte-regulated 4E, pseudogene; X-linked

lymphocyte-regulated 4B; X-linked lymphocyte-regulated 4C; hypothetical protein LOC100044049

Xlr5a 574438 4.63

X-linked lymphocyte-regulated 5B; X-linked lymphocyte-regulated 5D, pseudogene; X-linked lymphocyte-regulated 5A; X-linked lymphocyte-regulated 5E, pseudogene; predicted gene, EG667719

Xlr5b 627081 5.21

X-linked lymphocyte-regulated 5B; X-linked lymphocyte-regulated 5D, pseudogene; X-linked lymphocyte-regulated 5A; X-linked lymphocyte-regulated 5E, pseudogene; predicted gene, EG667719

Genes downregulated in TKO ESCs compared to wt ESCs Gene symbol Entrez

Gene ID Fold change

to wt ESCs Gene name

Atxn1l 52335 -1.01 ataxin 1-like

Clcn5 12728 -1.12 chloride channel 5

Cyr61 16007 -2.14 cysteine rich protein 61

Dnmt1 13433 -1.27 DNA methyltransferase (cytosine-5) 1 Dnmt3a 13435 -1.62 DNA methyltransferase 3A Dnmt3b 13436 -2.52 DNA methyltransferase 3B Dpysl2 12934 -1.23 dihydropyrimidinase-like 2 Fkbp10 14230 -1.02 FK506 binding protein 10

Fndc3c1 333564 -2.86 fibronectin type III domain containing 3C1 Gja1 14609 -1.18 gap junction protein, alpha 1

Krt18 16668 -2.46 keratin 18

Krt19 16669 -2.9 keratin 19

Lpar6 67168 -1.66 purinergic receptor P2Y, G-protein coupled, 5

Lphn2 99633 -1.86 latrophilin 2

Lrrc8c 100604 -1.44 leucine rich repeat containing 8 family, member C Mphosph6 68533 -1.03 M phase phosphoprotein 6; predicted gene 11448

Nes 18008 -1.9 nestin

Nnat 18111 -2.13 neuronatin

Ogfr 72075 -1.05 opioid growth factor receptor

Sema6a 20358 -2.38 sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A Sh3bgrl 56726 -1.02 SH3-binding domain glutamic acid-rich protein like

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Sox4 20677 -1 SRY-box containing gene 19; SRY-box containing gene 4

Tagln 21345 -2.29 transgelin

Thbs1 21825 -2.61 thrombospondin 1; similar to thrombospondin 1 Tlcd1 68385 -1.09 TLC domain containing 1

Concordant upregulated genes in dnmt1-/- and TKO ESCs compared to wt ESCs Gene symbol Entrez

Gene ID

Fold change dnmt1-/- to

wt ESCs

Fold change TKO to wt

ESCs Gene name

1700013H16Rik 75514 1.67 1.81 RIKEN cDNA 1700013H16 gene

AV320801 331531 2.85 3.61 expressed sequence AV320801

Dazl 13164 2.01 2.39 deleted in azoospermia-like

Dcdc2a 195208 1.34 1.52 doublecortin domain containing 2a

Dnajc5g 231098 1.36 1.71 DnaJ (Hsp40) homolog, subfamily C, member 5 gamma Efhc2 74405 3.44 3.58 EF-hand domain (C-terminal) containing 2

Fkbp6 94244 1.81 2.16 FK506 binding protein 6

Fthl17 83457 1.65 1.5 ferritin, heavy polypeptide-like 17

Gm13498 227885 1.83 2.38 predicted gene 13498

Gm2889 1000406

58 2.1 2.35

hypothetical protein LOC100041609; hypothetical protein LOC100044795;

predicted gene 3395; similar to gag polyprotein; hypothetical protein LOC100047557; hypothetical protein LOC100040347; hypothetical protein LOC100044384; hypothetical protein LOC100045342; hypothetical protein LOC100038979; predicted gene 2889

Gm5128 331529 3.08 3.91 predicted gene 7903; predicted gene 5128

Gpat2 215456 1.45 1.34 RIKEN cDNA A530057A03 gene

Gpx6 75512 1.23 1.43 glutathione peroxidase 6

Gtsf1 74174 1.67 1.59 gametocyte specific factor 1

Hormad1 67981 2.42 2.71 HORMA domain containing 1; predicted gene 7167

Magea1 17137 1.42 2.42 melanoma antigen, family A, 1

Nckap1l 105855 1.54 1.75 NCK associated protein 1 like Nlrp4c 83564 1.61 1.58 NLR family, pyrin domain containing 4C

Nxf3 245610 1.72 1.61 nuclear RNA export factor 3

Olfr307 258610 2.51 2.17 olfactory receptor 307 Pnma5 385377 1.58 1.62 paraneoplastic antigen family 5

Pramel3 83565 2.96 3.75 preferentially expressed antigen in melanoma-like 3

Rnf17 30054 1.28 1.06 ring finger protein 17

Scml2 107815 1.64 2.16 similar to sex comb on midleg-like 2 (Drosophila); sex comb on midleg-like 2 (Drosophila)

Smc1b 140557 1.4 2.47 structural maintenance of chromosomes 1B

Sohlh2 74434 1.05 1.53 spermatogenesis and oogenesis specific basic helix-loop-helix 2 Wfdc15a 68221 1.85 1.82 WAP four-disulfide core domain 15A

Xlr3a 22445 3.35 3.16

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked regulated 3A; X-linked regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr3b 574437 3.48 3.32

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked regulated 3A; X-linked regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr3c 22446 3.54 3.36

hypothetical protein LOC100044094; similar to X-linked lymphocyte-regulated protein 3A; X-linked lymphocyte-regulated 3E, pseudogene; hypothetical protein LOC100044314; similar to X-LINKED LYMPHOCYTE-REGULATED PROTEIN 3A (XLR RELATED PROTEIN A12); X-linked lymphocyte-regulated 3C; X-linked regulated 3A; X-linked regulated 3B; X-linked lymphocyte-regulated 3D, pseudogene

Xlr4b 27083 3.07 3.09

X-linked lymphocyte-regulated 4D; X-linked lymphocyte-regulated 4E, pseudogene;

X-linked lymphocyte-regulated 4B; X-linked lymphocyte-regulated 4C; hypothetical protein LOC100044049

Xlr4c 72891 3.36 3.34

X-linked lymphocyte-regulated 4D; X-linked lymphocyte-regulated 4E, pseudogene;

X-linked lymphocyte-regulated 4B; X-linked lymphocyte-regulated 4C; hypothetical protein LOC100044049

Xlr5a 574438 4.48 4.63

X-linked lymphocyte-regulated 5B; X-linked lymphocyte-regulated 5D, pseudogene;

X-linked lymphocyte-regulated 5A; X-linked lymphocyte-regulated 5E, pseudogene;

predicted gene, EG667719

Xlr5b 627081 5.05 5.21

X-linked lymphocyte-regulated 5B; X-linked lymphocyte-regulated 5D, pseudogene;

X-linked lymphocyte-regulated 5A; X-linked lymphocyte-regulated 5E, pseudogene;

predicted gene, EG667719

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Concordant downregulated genes in dnmt1-/- and TKO ESCs compared to wt ESCs Gene symbol Entrez

Gene ID

Fold change dnmt1-/- to

wt ESCs

Fold change TKO to wt

ESCs Gene name

Dnmt1 13433 -1.02 -1.27 DNA methyltransferase (cytosine-5) 1

Lphn2 99633 -1.53 -1.86 latrophilin 2

Sema6a 20358 -2.12 -2.38 sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A

6.2 Differentially regulated genes during the first differentiation period