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Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2

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Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 VTCN1 V-set domain containing T-cell activation inhibitor 1 -4.491 AMDHD1 amidohydrolase domain containing 1 -4.479 EDAR ectodysplasin A receptor -4.429 GTSF1 gametocyte specific factor 1 -4.429 KIAA0825 KIAA0825 -4.408 SLC26A7 solute carrier family 26 member 7 -4.343 LINC00639 long intergenic non-protein coding RNA 639 -4.298 ECM2 extracellular matrix protein 2 -4.241 C1QTNF7 C1q and TNF related 7 -4.228 LRRK1 leucine rich repeat kinase 1 -4.228 LRRC18 leucine rich repeat containing 18 -4.191 NDP NDP, norrin cystine knot growth factor -4.184 B3GALT2 beta-1,3-galactosyltransferase 2 -4.158 GLI1 GLI family zinc finger 1 -4.154 LINC01126 long intergenic non-protein coding RNA 1126 -4.154 INPP1 inositol polyphosphate-1-phosphatase -4.154 FAM92B family with sequence similarity 92 member B -4.132 ANXA13 annexin A13 -4.102 CYP3A7 cytochrome P450 family 3 subfamily A member 7 -4.096 PGM5-AS1 PGM5 antisense RNA 1 -4.089 NGFR nerve growth factor receptor -4.076 COL9A3 collagen type IX alpha 3 chain -4.067 RSPO2 R-spondin 2 -4.031 AIG1 androgen induced 1 -3.993 ARSF arylsulfatase F -3.993 TLE6 transducin like enhancer of split 6 -3.93 RAB37 RAB37, member RAS oncogene family -3.906 FABP6 fatty acid binding protein 6 -3.903 PLXDC1 plexin domain containing 1 -3.883 FOLH1 folate hydrolase 1 -3.86 SCN9A sodium voltage-gated channel alpha subunit 9 -3.813 CFD complement factor D -3.813 NPY1R neuropeptide Y receptor Y1 -3.813 TCEAL2 transcription elongation factor A like 2 -3.813 LINC00626 long intergenic non-protein coding RNA 626 -3.808 LINC00890 long intergenic non-protein coding RNA 890 -3.774 IL33 interleukin 33 -3.764 SIGLEC1 sialic acid binding Ig like lectin 1 carcinoembryonic antigen related cell adhesion -3.739 CEACAM1 molecule 1 -3.713 LEFTY1 left-right determination factor 1 -3.713 P2RX5 purinergic receptor P2X 5 -3.713 SYN3 synapsin III -3.713 PLA2G5 phospholipase A2 group V -3.687 FABP7 fatty acid binding protein 7 -3.685 CSRNP3 cysteine and serine rich nuclear protein 3 -3.674 FAM213A family with sequence similarity 213 member A -3.664 ADAM12 ADAM metallopeptidase domain 12 immunoglobulin superfamily DCC subclass member -3.661 IGDCC4 4 -3.661 SKAP1 src kinase associated phosphoprotein 1 -3.639 PLA1A phospholipase A1 member A -3.638 KANK4 KN motif and ankyrin repeat domains 4 -3.63 MXD3 MAX dimerization protein 3 -3.606 LOC101927780 uncharacterized LOC101927780 -3.606 MGST2 microsomal glutathione S-transferase 2 -3.606 HPSE2 heparanase 2 (inactive) -3.569 PLA2G2A phospholipase A2 group IIA -3.563 AGAP2 ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 -3.55 CYP39A1 cytochrome P450 family 39 subfamily A member 1 -3.55 RBFOX3 RNA binding protein, fox-1 homolog 3 -3.55 PIH1D2 PIH1 domain containing 2 -3.53 SULT1A1 sulfotransferase family 1A member 1 -3.521 MAPK15 mitogen-activated protein kinase 15 -3.491 CILP cartilage intermediate layer protein -3.491 FAM110D family with sequence similarity 110 member D -3.491 ZNF586 zinc finger protein 586 -3.491 SCNN1D sodium channel epithelial 1 delta subunit -3.491 SPATA16 spermatogenesis associated 16 -3.491 NBAT1 neuroblastoma associated transcript 1 -3.491 TNNI1 troponin I1, slow skeletal type -3.491 FSTL4 follistatin like 4 -3.491 ANO2 anoctamin 2 -3.491 KBTBD13 kelch repeat and BTB domain containing 13 -3.471 ENDOU endonuclease, poly(U) specific immunoglobulin superfamily DCC subclass member -3.452 IGDCC3 3 CKLF like MARVEL transmembrane domain -3.429 CMTM5 containing 5 -3.408 BCL11A B-cell CLL/lymphoma 11A -3.398 SPARCL1 SPARC like 1 -3.385 LAMA5 laminin subunit alpha 5 -3.368 TMEM100 transmembrane protein 100 -3.365 ARHGEF15 Rho guanine nucleotide exchange factor 15 -3.365 FAAH2 fatty acid amide hydrolase 2 -3.365 IZUMO1 izumo sperm-egg fusion 1 DnaJ heat shock protein family (Hsp40) member C5 -3.365 DNAJC5B beta -3.365 NLGN1 neuroligin 1 -3.365 TNNI2 troponin I2, fast skeletal type -3.352 GALNT16 polypeptide N-acetylgalactosaminyltransferase 16 H19, imprinted maternally expressed transcript (non- -3.337 H19 protein coding) -3.321 TM7SF2 transmembrane 7 superfamily member 2 -3.312 HHIP hedgehog interacting protein -3.305 CFI complement factor I -3.298 NTN3 netrin 3 -3.298 MMP28 matrix metallopeptidase 28 -3.298 HTR2A 5-hydroxytryptamine receptor 2A -3.268 CDA cytidine deaminase -3.263 NOXA1 NADPH oxidase activator 1 -3.256 FZD10-AS1 FZD10 antisense RNA 1 (head to head) -3.228 MAMDC4 MAM domain containing 4 -3.228 LOC100631378 uncharacterized 100631378 -3.228 ZNF781 zinc finger protein 781 -3.228 TBX6 T-box 6 -3.228 TEK TEK receptor tyrosine kinase -3.228 MYL4 myosin light chain 4 -3.207 HOXB-AS3 HOXB cluster antisense RNA 3 -3.187 MEOX1 mesenchyme homeobox 1 -3.179 LDHD lactate dehydrogenase D -3.179 CA11 carbonic anhydrase 11 -3.176 CYTL1 cytokine like 1 -3.168 SORCS2 sortilin related VPS10 domain containing receptor 2 -3.165 TEX19 testis expressed 19 -3.154 SPTBN5 spectrin beta, non-erythrocytic 5 -3.154 GMPR guanosine monophosphate reductase -3.132 PIDD1 p53-induced death domain protein 1 -3.128 ODF3L1 outer dense fiber of sperm tails 3 like 1 -3.125 NDST4 N-deacetylase and N-sulfotransferase 4 -3.118 BCHE butyrylcholinesterase -3.115 ADAM21 ADAM metallopeptidase domain 21 -3.115 ARHGAP15 Rho GTPase activating protein 15 -3.104 OLFML1 olfactomedin like 1 -3.094 LSP1 lymphocyte-specific protein 1 -3.093 SULF2 sulfatase 2 -3.09 ABCA7 ATP binding cassette subfamily A member 7 -3.089 ADRA2A adrenoceptor alpha 2A -3.076 GPC3 glypican 3 -3.076 C12orf60 chromosome 12 open reading frame 60 -3.076 BAALC-AS1 BAALC antisense RNA 1 -3.076 CAMKV CaM kinase like vesicle associated -3.076 RANBP3L RAN binding protein 3 like -3.076 MB myoglobin -3.076 SYNGR4 synaptogyrin 4 -3.076 RIBC1 RIB43A domain with coiled-coils 1 -3.076 KLHL6 kelch like family member 6 -3.076 NAPA-AS1 NAPA antisense RNA 1 -3.076 CNFN cornifelin -3.076 GPM6A glycoprotein M6A -3.074 RNF112 ring finger protein 112 -3.049 LPAR3 lysophosphatidic acid receptor 3 ADAM metallopeptidase with thrombospondin type 1 -3.029 ADAMTS17 motif 17 -3.021 LINC00896 long intergenic non-protein coding RNA 896 -3.021 CALY calcyon neuron specific vesicular protein -3.021 MYL10 myosin light chain 10 ST8 alpha-N-acetyl-neuraminide alpha-2,8- -3.016 ST8SIA1 sialyltransferase 1 -3.013 FREM1 FRAS1 related extracellular matrix 1 -3.004 METTL7A methyltransferase like 7A amyotrophic lateral sclerosis 2 chromosome region 3.001 ALS2CR12 12 3.001 BIRC3 baculoviral IAP repeat containing 3 3.007 PVR poliovirus receptor 3.015 ADRA2B adrenoceptor alpha 2B 3.016 PERP PERP, TP53 apoptosis effector 3.026 PDK4 pyruvate dehydrogenase kinase 4 3.033 CRIM1 cysteine rich transmembrane BMP regulator 1 3.033 HTR2B 5-hydroxytryptamine receptor 2B 3.041 SERPINE1 serpin family E member 1 3.042 TNFSF9 TNF superfamily member 9 3.042 CD55 CD55 molecule (Cromer blood group) ADAM metallopeptidase with thrombospondin type 1 3.044 ADAMTS1 motif 1 3.048 UPP1 uridine phosphorylase 1 3.048 STX11 syntaxin 11 3.049 FTH1 ferritin heavy chain 1 3.054 DGKI diacylglycerol kinase iota 3.054 RIPK2 receptor interacting serine/threonine kinase 2 3.057 ARSJ arylsulfatase family member J 3.064 VGF VGF nerve growth factor inducible RRN3 homolog, RNA polymerase I transcription 3.068 RRN3P3 factor pseudogene 3 3.091 PMAIP1 phorbol-12-myristate-13-acetate-induced protein 1 3.094 ANGPT2 angiopoietin 2 3.094 FKBP1B FK506 binding protein 1B 3.094 TAS2R4 taste 2 receptor member 4 3.094 FCER1G Fc fragment of IgE receptor Ig 3.094 TMPRSS9 transmembrane protease, serine 9 3.094 ALDH8A1 aldehyde dehydrogenase 8 family member A1 3.094 SLC2A5 solute carrier family 2 member 5 3.094 mir-24 microRNA 24-1 3.094 NUAK1 NUAK family kinase 1 3.094 SELPLG selectin P ligand 3.094 IRF5 interferon regulatory factor 5 3.094 LINC00571 long intergenic non-protein coding RNA 571 3.094 PSG4 pregnancy specific beta-1-glycoprotein 4 3.094 CXCL10 C-X-C motif chemokine ligand 10 3.094 ZFPM2 zinc finger protein, FOG family member 2 ankyrin repeat and sterile alpha motif domain 3.094
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  • Supplemental Information

    Supplemental Information

    Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig.
  • CDH12 Cadherin 12, Type 2 N-Cadherin 2 RPL5 Ribosomal

    CDH12 Cadherin 12, Type 2 N-Cadherin 2 RPL5 Ribosomal

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