Supplementary table 4: Genes down- and up-regulated after culture in KSOM vs VIVO Fold change Gene symbol Description Affymetrix number -20.25 Rassf4 Ras association (RalGDS/AF-6) domain family 4 1444009_at -14.06 Bhmt2 betaine-homocysteine methyltransferase 2 1418914_s_at -10.56 Akp5 alkaline phosphatase 5 1450635_at -7.02 Socs3 suppressor of cytokine signaling 3 1455899_x_at -5.76 Nucb2 nucleobindin 2 1418355_at -5.76 Stmn3 stathmin-like 3 1435113_x_at -5.29 Bhmt betaine-homocysteine methyltransferase 1450624_at -5.29 Akr1c21 aldo-keto reductase family 1, member C21 1451030_at -5.06 Bmp4 bone morphogenetic protein 4 1422912_at -4.62 Fgf4 fibroblast growth factor 4 1420085_at -4.62 Cbfa2t1h CBFA2T1 identified gene homolog (human) 1444615_x_at -4.41 Arf7 ADP-ribosylation factor 7 1430234_at -4.20 Tmem64 transmembrane protein 64 1434307_at -4.20 Cpxm1 carboxypeptidase X 1 (M14 family) 1448901_at -4.20 Apcdd1 adenomatosis polyposis coli down-regulated 1 1454822_x_at -4.00 Dmgdh dimethylglycine dehydrogenase precursor 1452311_at -3.61 Morc1 microrchidia 1 1419418_a_at -3.61 Tmem64 transmembrane protein 64 1433735_a_at -3.61 Parvb Parvin, beta (Parvb), mRNA 1438672_at -3.61 Akp5 alkaline phosphatase 5 1450636_s_at -3.42 Cebpa CCAAT/enhancer binding protein (C/EBP), alpha 1418982_at -3.24 --- Transcribed locus 1448021_at -3.06 Snap91 synaptosomal-associated protein 91 1416688_at -2.89 MGI:1919030 myo-inositol 1-phosphate synthase A1 1415977_at -2.89 --- RNA transcript from U17 small nucleolar RNA host gene 1433789_at -2.56 Tspan1 tetraspan 1 1417957_a_at -2.56 4921530G04Rik RIKEN cDNA 4921530G04 gene 1460274_at -2.40 Tcl1 T-cell lymphoma breakpoint 1 1422458_at -2.40 Fasn fatty acid synthase 1423828_at -2.25 Tex19 testis expressed gene 19 1417482_at -2.25 Ube2a ubiquitin-conjugating enzyme E2A, RAD6 homolog (S. cerevisiae) 1417609_at -2.25 Tmepai transmembrane, prostate androgen induced RNA 1422706_at -2.25 Pnliprp2 pancreatic lipase-related protein 2 1437438_x_at -1.96 Wrnip1 Werner helicase interacting protein 1 1448376_at -1.82 Sox2 SRY-box containing gene 2 1416967_at -1.82 Pias2 protein inhibitor of activated STAT 2 1428725_at -1.82 Cxxc6 CXXC finger 6 1429448_s_at -1.82 Tmcc3 transmembrane and coiled coil domains 3 1435554_at -1.82 Slc16a10 solute carrier family 16 (monocarboxylic acid transporters), member 10 1436368_at -1.82 Rrbp1 ribosome binding protein 1 1449221_a_at -1.69 Fscn1 fascin homolog 1, actin bundling protein (Strongylocentrotus) purpuratus) 1416514_a_at -1.69 Glt28d1 glycosyltransferase 28 domain containing 1 1418681_at -1.69 Kcmf1 potassium channel modulatory factor 1 1418694_at -1.69 Rpl13a ribosomal protein L13a 1433928_a_at -1.69 Lhfpl2 lipoma HMGIC fusion partner-like 2 1434129_s_at -1.69 --- Mus musculus, clone IMAGE:4219318, mRNA 1442003_at -1.69 Upp1 uridine phosphorylase 1 1448562_at -1.69 Ssx2ip synovial sarcoma, X breakpoint 2 interacting protein 1448743_at -1.69 D11Ertd759e DNA segment, Chr 11, ERATO Doi 759, expressed 1455500_at -1.56 Tpst1 protein-tyrosine sulfotransferase 1 1421733_a_at -1.56 Rpl5 ribosomal protein L5 /// similar to 60S ribosomal protein L5 /// similar to 60S ribosomal protein L5 1423666_s_at -1.56 S100a16 S100 calcium binding protein A16 1425560_a_at -1.56 Wdr40b WD repeat domain 40B 1434170_at -1.56 2310007O11Rik RIKEN cDNA 2310007O11 gene 1436446_at -1.56 Map4k4 mitogen-activated protein kinase 4 1448050_s_at -1.56 Ddx21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 1448271_a_at -1.56 Pycr2 pyrroline-5-carboxylate reductase family, member 2 1448315_a_at -1.56 5730557B15Rik RIKEN cDNA 5730557B15 gene 1453287_at -1.56 Wdr6 WD repeat domain 6 1455940_x_at -1.56 Ccbl2 cysteine conjugate-beta lyase 2 1455991_at -1.44 Scd2 stearoyl-Coenzyme A desaturase 2 1415824_at -1.44 Satb1 special AT-rich sequence binding protein 1 1416007_at -1.44 Gclc glutamate-cysteine ligase, catalytic subunit 1424296_at -1.44 Phf3 PHD finger protein 3 1429000_at -1.44 Eomes eomesodermin homolog (Xenopus laevis) 1435172_at -1.44 Pfkl phosphofructokinase, liver, B-type 1439148_a_at -1.44 Chka choline kinase alpha 1450264_a_at -1.44 Ckb creatine kinase, brain 1455106_a_at -1.44 LOC545325 hypothetical protein LOC545325 1455604_at -1.44 Dus3l dihydrouridine synthase 3-like (S. cerevisiae) 1459805_x_at -1.32 Sms spermine synthase 1421052_a_at -1.32 Slc25a20 solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20 1423108_at -1.32 Ldlrap1 low density lipoprotein receptor adaptor protein 1 1424378_at -1.32 4121402D02Rik RIKEN cDNA 4121402D02 gene 1428873_a_at -1.32 D6Ertd253e DNA segment, Chr 6, ERATO Doi 253, expressed 1433509_s_at -1.32 Dpp7 dipeptidylpeptidase 7 1436479_a_at -1.32 Kpnb1 karyopherin (importin) beta 1 1448526_at -1.32 Usp25 ubiquitin specific peptidase 25 1448939_at -1.32 BB001228 expressed sequence BB001228 1455425_at -1.21 Oact2 O-acyltransferase (membrane bound) domain containing 2 1425029_a_at -1.21 9430034D17Rik RIKEN cDNA 9430034D17 gene, mRNA (cDNA clone IMAGE:30109386) 1434398_at -1.21 --- --- 1440253_at -1.21 Tial1 Tial1 cytotoxic granule-associated RNA binding protein-like 1 1452821_at -1.21 BC021395 cDNA sequence BC021395 1454964_at -1.10 Nfxl1 nuclear transcription factor, X-box binding-like 1 1417145_at -1.10 Klf4 Kruppel-like factor 4 (gut) 1417394_at -1.10 Dgat1 diacylglycerol O-acyltransferase 1 1418295_s_at -1.10 0610039J04Rik RIKEN cDNA 0610039J04 gene 1428798_s_at -1.10 Tmem57 transmembrane protein 57 1428883_at -1.10 Sema5a sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) 1437422_at -1.10 --- --- 1438962_s_at -1.10 4930453N24Rik RIKEN cDNA 4930453N24 gene 1449718_s_at -1.10 Tdgf1 teratocarcinoma-derived growth factor 1450989_at -1.10 Pten phosphatase and tensin homolog 1455728_at -1.00 Trrap transformation/transcription domain-associated protein 1416532_at -1.00 Rpl22l1 ribosomal protein L22 like 1 1417126_a_at -1.00 Rpl14 ribosomal protein L14 1422128_at -1.00 4930517K11Rik RIKEN cDNA 4930517K11 gene 1423327_at -1.00 2700078E11Rik RIKEN cDNA 2700078E11 gene 1424983_a_at -1.00 Eomes eomesodermin homolog (Xenopus laevis) 1426001_at -1.00 Axin1 axin 1 1426966_at -1.00 Nfx1 nuclear transcription factor, X-box binding 1 1428248_at -1.00 1300004G08Rik RIKEN cDNA 1300004G08 gene /// similar to hypothetical protein LOC65259 1428565_at -1.00 --- --- 1429321_at -1.00 Cct4 chaperonin subunit 4 (delta) 1430034_at -1.00 6720458F09Rik RIKEN cDNA 6720458F09 gene 1433962_at -1.00 Cds2 CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2 1434256_s_at -1.00 1110064P04Rik RIKEN cDNA 1110064P04 gene 1435160_at -1.00 Phtf2 putative homeodomain transcription factor 2 1437067_at -1.00 Noc4l nucleolar complex associated 4 homolog (S. cerevisiae) 1443794_x_at -1.00 Akap1 A kinase (PRKA) anchor protein 1 1449019_at -1.00 Fxr1h fragile X mental retardation gene 1, autosomal homolog 1452247_at -0.90 Ncl nucleolin 1415772_at -0.90 Crip1 cysteine-rich protein 1 (intestinal) 1416326_at -0.90 Surf6 surfeit gene 6 1416864_at -0.90 Npepps aminopeptidase puromycin sensitive 1417385_at -0.90 Epb4.1l4b erythrocyte protein band 4.1-like 4b 1418294_at -0.90 D11Ertd707e DNA segment, Chr 11, ERATO Doi 707, expressed 1418543_s_at -0.90 Smad4 MAD homolog 4 (Drosophila) 1422486_a_at -0.90 0610039J04Rik RIKEN cDNA 0610039J04 gene 1428797_at -0.90 Tor2a torsin family 2, member A 1438547_x_at -0.90 Gna13 guanine nucleotide binding protein, alpha 13 1450656_at -0.90 Wdr79 WD repeat domain 79 1456724_x_at -0.90 Chordc1 cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1 1460645_at -0.81 Gna13 guanine nucleotide binding protein, alpha 13 1422555_s_at -0.81 D10Ucla1 DNA segment, Chr 10, University of California at Los Angeles 1 1424780_a_at -0.81 Etv5 ets variant gene 5 1428142_at -0.81 AU020206 expressed sequence AU020206 1433935_at -0.81 Dhps deoxyhypusine synthase 1434003_a_at -0.81 Gprk6 G protein-coupled receptor kinase 6 1437436_s_at -0.81 AI326906 Nucleolar complex associated 4 homolog (S. cerevisiae) (Noc4l), mRNA 1438095_x_at -0.81 Htra1 HtrA serine peptidase 1 1438251_x_at -0.81 Nuak1 ZNUAK family, SNF1-like kinase, 1 1438684_at -0.81 Cds2 CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2 1438957_x_at -0.81 Srpk1 serine/arginine-rich protein specific kinase 1 1455107_at -0.81 Chd1 chromodomain helicase DNA binding protein 1 1457473_at -0.72 Etv3 ets variant gene 3 1418635_at -0.72 LOC433829 similar to Piwi/Argonaute family protain meIF2C1 1434331_at -0.72 BC005537 cDNA sequence BC005537 1423154_at -0.72 Gnpnat1 glucosamine-phosphate N-acetyltransferase 1 1423158_at -0.72 Ddx26 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26 1423275_at -0.72 Ubxd4 UBX domain containing 4 1425019_at -0.72 Narg1l NMDA receptor regulated 1-like 1429057_at -0.72 Kbtbd8 kelch repeat and BTB (POZ) domain containing 8 1433902_at -0.72 Ampd2 adenosine monophosphate deaminase 2 (isoform L) 1438941_x_at -0.72 Tnks2 tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2 1447522_s_at -0.72 Usp10 ubiquitin specific peptidase 10 1448230_at -0.72 Picalm phosphatidylinositol binding clathrin assembly protein 1451316_a_at -0.72 Hspa1a heat shock protein 1A 1452318_a_at -0.72 Cggbp1 CGG triplet repeat binding protein 1 1454641_at -0.72 Ibtk inhibitor of Bruton agammaglobulinemia tyrosine kinase 1454905_at -0.72 Grwd1 glutamate-rich WD repeat containing 1 1455841_s_at -0.64 1110005A23Rik RIKEN cDNA 1110005A23 gene 1416095_x_at -0.64 Htra1 HtrA serine peptidase 1 1416749_at -0.64 Dnajb1 DnaJ (Hsp40) homolog,