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Table 4.

Fold changes in gene expression in early prism larvae (40 h post-fertilization) that developed under High CO2 conditions compared with early prism larvae raised under Control CO2conditions

GeneGene IDFold change (FCUL → FCLL)Protein information
Acid–base and ion regulation    
   Slc8a3 SPU_026183 –1.52 → –1.02 Na+/Ca2+ exchanger 
   Slc41a1 SPU_001481 –1.35 → –1.13 mgtE-like Mg2+ transporter 
   Scnn1a SPU_014519 –1.43 → –1.07 Sodium channel 
   Aqp SPU_023979 –1.40 → –1.09 Aquaporin, water channel 
   Slc12a2 SPU_004877 –1.35 → –1.12 Na+/K+/2Cl cotransporter 
   Slco5a1 SPU_004407 –1.29 → –1.06 Organic anion transporter 
   Slc39a3 SPU_002226 –1.38 → –1.02 Zinc transporter 
   Slc24a4 SPU_023689 –1.37 → +1.03 Na+/K+/Ca2+ exchanger 
   Slco SPU_007603 –1.31 → –1.01 Organic anion transporter 
   Slc39a8 SPU_023011 –1.33 → +1.02 Zinc transporter 
   Atp13a4 SPU_005539 –1.26 → –1.03 H+/K+-ATPase 
   Slc20a2 SPU_020699 –1.30 → +1.02 Na-phosphate transporter, type III 
   Atp2a1 SPU_013051 –1.20 → –1.06 Ca2+-ATPase 
   Slc5a8 SPU_012573 –1.30 → –1.06 Na+-iodide related transporter 
   Slc5a5 SPU_021781 –1.36 → +1.02 Na+-iodide symporter 
   Aqp* SPU_021388 +1.46 → +1.07 Aquaporin, water channel and potentially CO2 
Apoptosis    
   Caspase 8-like2a SPU_008540 –1.27 → –1.04 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 8-like2b SPU_022177 –1.29 → 1.00 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 8-like3* SPU_016039 –1.28 → –1.18 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 8-like5 SPU_024371 –1.36 → +1.05 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 3/7-like SPU_002280 –1.33 → –1.05 Cysteine protease, last caspase in pathway before cell death 
   caspase N2a SPU_009497 –1.26 → –1.03 Cysteine protease, N for novel 
   caspase N2f SPU_026743 –1.32 → –1.01 Cysteine protease, N for novel 
   caspase N3a SPU_017523 –1.46 → +1.02 Cysteine protease, N for novel 
   caspase N6a SPU_006866 –1.37 → +1.02 Cysteine protease, N for novel 
   caspase N6b SPU_027596 –1.27 → –1.03 Cysteine protease, N for novel 
   ICE like-1a SPU_002921 –1.75 → +1.26 Interleukin-converting enzyme, cysteine protease 
   ICE like-2 SPU_021141 –1.28 → –1.08 Interleukin-converting enzyme, cysteine protease 
   ICE like-3 SPU_011872 –1.32 → –1.04 Interleukin-converting enzyme, cysteine protease 
   ICE like-4 SPU_012722 –1.34 → –1.08 Interleukin-converting enzyme, cysteine protease 
   Tnfsf-like3 SPU_015654 –1.32 → –1.02 Tumor necrosis factor subfamily like 3, ligand for TNFR with death domain 
   Tnfsf-like1 SPU_009528 –1.38 → +1.04 Tumor necrosis factor subfamily like 1, ligand for TNFR lacking death domain 
   Tnfrsf1a SPU_012211 –1.38 → +1.01 Tumor necrosis factor receptor (TNFR) superfamily 1, trigger apoptosis upon binding of Ligand (TNF) 
   Tnfrsf-like1 SPU_010230 –1.28 → –1.06 TNFR 
   Tnfrsf-cl1 SPU_010180 –1.36 → 1.00 TNFR, lacks death domain 
   HVEM/Eda2r-like 1 SPU_024584 –1.37 → +1.01 TNFR, lacks death domain 
   Troy/Eda2r-like 2 SPU_020740 –1.42 → +1.05 TNFR, lacks death domain 
   TRAF3 SPU_026495 –1.64 → +1.09 Tnf receptor-associated factor 3, adaptor without death domain 
   TRAF4 SPU_008332 –1.38 → –1.02 Adaptor without death domain 
   TRAF6 SPU_028898 –1.47 → +1.08 Adaptor without death domain 
   BIRC2b SPU_014057 –1.39 → –1.05 Baculoviral IAP repeat-containing 2, anti-apoptotic 
   BOK SPU_021416 –1.33 → –1.05 Bcl2-related ovarian killer, pro-apoptotic 
   IAP1 SPU_014350 –1.39 → +1.04 Inhibitor of apoptosis 1, anti-apoptotic 
   Mil2 SPU_001916 –1.40 → +1.05 Bcl-2 protein, pro-apoptotic 
   Slc22a13 SPU_017736 –1.35 → +1.02 Organic anion transporter, involved in apoptosis 
   Slc22a15 SPU_019637 –1.24 → –1.05 Organic anion transporter, involved in apoptosis 
Biomineralization    
   MSP130* SPU_013821 –1.42 → –1.05 Primary mesenchyme cell (PMC)-specific protein, cell surface 
   MSP130-related 6 SPU_014492 –1.31 → –1.02 PMC-specific protein 
   Runt-2 SPU_007852 –1.34 → –1.09 Transcription factor, triggers differentiation of skeletogenic cells 
   Alx1 SPU_022817 –1.37 → –1.05 PMC-specific protein, required for skeleton formation 
   serine rich protein 12 SPU_015338 –1.31 → –1.01 Glycoprotein that binds calcium 
   SPARC-like SPU_012548 –1.46→ +1.10 Secreted protein acidic and rich in cysteine, binds Ca2+ 
   Casr SPU_0017585 –1.26→ –1.04 Calcium receptor 
   CA-4 likeB SPU_022346 –1.38 → +1.04 Carbonic anhydrase, catalyzes reversible hydration of CO2 to bicarbonate and protons 
   CA-10 like SPU_0004135 –1.31→ 1.00 Carbonic anhydrase 
   CA-8 likeB SPU_026483 –1.23→ –1.06 Carbonic anhydrase 
   CA-12 likeB SPU_025722 –1.21→ –1.06 Carbonic anhydrase 
   CA-7 likeA SPU_012518 +1.55→ +1.03 Carbonic anhydrase, extracellular 
Cell cycle    
   Cdc23/Apc8 SPU_012696 –1.72 → –1.24 Cell division cycle 23, ubiquitin-proteolysis pathway 
   Slc29a4 SPU_008397 –1.47 → –1.10 Nucleoside transporter 
   Slc28a2 SPU_025779 –1.38 → –1.01 Na+-coupled nucleoside transporter 
   Apc11 SPU_021695 –1.28 → –1.07 Anaphase promoting complex 11, ubiquitin-proteolysis pathway 
   Myt1 SPU_008280 –1.32 → –1.04 Tyrosine kinase, inhibits cylin dependent kinase 1 
   PFAIRE SPU_003654 –1.46 → +1.07 Cyclin dependent kinase 
   Neka SPU_017790 –1.41 → +1.07 NIMA related kinase, mitotic kinase 
   SMC1 SPU_021629 +1.46 → +1.05 Structural maintenance of chromosome 1, condensin/cohesin complexes 
   SMC4* SPU_013617 +1.31 → 1.00 Structural maintenance of chromosome 4, condensin/cohesin complexes 
Cellular stress defensome    
   Protein homeostasis    
      Hsp100B SPU_006012 –1.44 → +1.04 100kDa heat shock protein, molecular chaperone 
      Hsp701B SPU_005808 –1.36 → +1.01 70kDa heat shock protein, molecular chaperone 
      Hsp701F SPU_013289 –1.26 → –1.04 70kDa heat shock protein, molecular chaperone 
      Hsp703A SPU_014864 –1.33 → 1.00 70kDa heat shock protein, molecular chaperone 
      Hsp70–like SPU_021458 –1.32 → +1.03 70kDa heat shock protein, molecular chaperone 
      Hsp20.1 SPU_001357 –1.19 → –1.12 20kDa heat shock protein, molecular chaperone 
      Hsp20.2 SPU_020294 –1.32 → 1.00 20kDa heat shock protein, molecular chaperone 
      UBXD1 SPU_012427 –1.33 → –1.02 UBX domain containing 1, Ub-proteasome pathway 
      ubiquitin SPU_015276 +1.38 → +1.15 Ubiquitin-proteasome pathway, signaling 
      Hsp40A* SPU_016562 +1.39 → +1.08 40kDa heat shock protein, co-chaperone of Hsp70 
   Antioxidant defense    
      Maf SPU_025888 –1.36 → –1.07 Transcription factor, oxidative stress-responsive 
      MGST-2 SPU_008286 –1.48 → +1.08 Glutathione S-transferase, microsomal 
      GST-12 SPU_023664 –1.32 → 1.00 Glutathione S-transferase, cytosolic 
      Gpx1 SPU_004397 –1.42 → +1.05 Glutathione peroxidase 7 
   Toxicant, metal and xenobiotic defense    
      Akr1a-like SPU_027986 –1.31 → –1.10 Aldo-keto reductase 
      Akr1b-like2 SPU_016996 –1.33 → –1.10 Aldo-keto reductase 
      Akr1b-like3 SPU_018466 –1.54 → +1.14 Aldo-keto reductase 
      Cyp2-like9* SPU_003606 –1.36 → –1.07 Cytochrome P450 monooxygenase, iron homeostasis 
      Cyp3-like8 SPU_016056 –1.38 → –1.01 Cytochrome P450 monooxygenase 
      Cyp4-like5 SPU_007558 –1.37 → +1.02 Cytochrome P450 monooxygenase 
      Cyp2-like14 SPU_006574 –1.21 → –1.08 Cytochrome P450 monooxygenase 
      Fmo5 SPU_022596 –1.26 → –1.08 Flavin-containing monooxygenase 5 
      Fmo3 SPU_022597 –1.35 → +1.02 Flavin-containing monooxygenase 3 
      ABCC9i SPU_018527 –1.39 → –1.02 ATP-binding cassette superfamily, efflux transporter 
      ABCG2 SPU_024785 –1.37 → 1.00 ATP-binding cassette superfamily, efflux transporter 
      Aldh3a1 SPU_009853 –1.32 → 1.00 Aldehyde dehydrogenase 
      Nat-like SPU_012976 –1.20 → –1.09 N-acyltransferase-like 
      NR1H6a SPU_017404 –1.31 → –1.09 Nuclear receptor subfamily 1 H member 6a 
      Ark1b-like4 SPU_028344 +1.46 → +1.05 Aldo-keto reductase 
      Fth1 SPU_004876 +1.52 → +1.07 Heavy chain of ferritin, iron storage 
      Fmo2 SPU_014947 +1.21 → +1.09 Flavin-containing monooxygenase 2 
   Adrenergic stress response    
      nAChR α7 SPU_013095 –1.37 → –1.01 Acetylcholine receptor, nicotinic 
      nAChR α9 SPU_005670 –1.36 → +1.00 Acetylcholine receptor, nicotinic 
      nAChR α4 SPU_019711 –1.56 → +1.17 Acetylcholine receptor, nicotinic 
      mAChR M5 SPU_016177 –1.45 → +1.07 Acetylcholine receptor, muscarinic 
      mAChR M4 SPU_019228 –1.30 → –1.02 Acetylcholine receptor, muscarinic 
      Slc22a3 SPU_006524 –1.39 → –1.04 Monoamine transporter, extraneuronal 
      Slc6a2 SPU_022506 –1.35 → +1.05 Sodium-dependent noradrenaline transporter 
      calcineurin SPU_018404 –1.25 → –1.08 Activates transcription of interleukin 2 
      SNAP-25 SPU_006859 –1.27 → –1.02 Synaptosome-associated protein 
Development    
   FoxB SPU_004551 –1.20 → –1.10 Forkhead box B, transcription factor 
   Trh SPU_014249 –1.29 → 1.00 Neuronal PAS domain protein 
   early-histone-H2a SPU_002577 +1.62 → +1.03 Involved in nucleosome assembly 
   FoxQ2 SPU_019002 +1.43 → +1.30 Forkhead box Q2, involved in axis specification 
   Not SPU_002129 +1.42 → +1.03 Transcription factor involved in differentiation 
   PKS-like* SPU_002895 +1.41 → +1.05 Polyketide synthase, pigment synthesis 
   Eve SPU_012253 +1.39 → +1.08 Even-skipped, body morphogenesis 
   Hes SPU_021608 +1.28 → +1.14 Hairy/enhancer of split, role in skeletogenic GRN 
   Otx SPU_010424 +1.40 → –1.04 Orthodenticle homeobox, role in endomesoderm GRN 
Kinome    
   FAK SPU_019686 –1.30 → –1.11 Focal adhesion kinase, cytoskeletal kinase 
   KIS SPU_027616 –1.32 → –1.09 Kinase interacting stathmin, cytoskeletal kinase 
   MLCKb SPU_000442 –1.37 → –1.04 Myosin light chain kinase, cytoskeletal kinase 
   projectin SPU_013917 –1.33 → –1.06 Cytoskeletal kinase 
   MAPKAPK5a SPU_013910 –1.24 → –1.14 Mitogen-activated protein kinase signaling 
   JAK2 SPU_020082 –1.47 → +1.06 Janus kinase 2, receptor signaling 
   JAK1 SPU_022495 –1.34 → –1.02 Janus kinase 1, receptor signaling 
   titin SPU_005613 –1.23 → –1.11 Cytoskeletal kinase 
   RIPK1-4A SPU_005215 –1.27 → –1.06 Receptor-interacting protein kinase, death kinase 
   LIMK SPU_022207 –1.56 → +1.17 LIM domain kinase, cytoskeletal kinase 
   ULK3 SPU_017980 –1.26 → –1.05 Unc-51-like kinase 3, cytoskeletal kinase 
Metabolism    
   Energy metabolism    
      Slc25a5* SPU_004813 –1.92 → –1.17 ADP, ATP carrier protein 2, energy transfer 
      Slc25a21 SPU_006682 –1.41 → +1.06 Mitochondrial oxodicarboxylate carrier, energy transfer 
      Atp5b SPU_005296 +1.51 → –1.01 ATP synthase, H+ transporting, F1 complex 
   Carbohydrate metabolism    
      glycosidase SPU_010831 –1.38 → –1.08 Glycosidase, degrades complex carbohydrates 
      β-d-xylosidase SPU_021638 –1.34 → 1.00 β-d-xylosidase, glycosidase 
      Ldh-d SPU_026206 –1.24 → –1.08 Lactate dehydrogenase d, anaerobic glycolysis 
      Mdh-1 SPU_023277 –1.33 → +1.05 Malate dehydrogenase 1, citric acid cycle 
      Pgm SPU_024573 –1.29 → –1.01 Phosphoglycerate mutase, glycolysis 
      Pgm2-like1 SPU_028876 –1.51 → +1.13 Phosphoglycerate mutase 2-like 1, glycolysis 
      Slc5a9 SPU_021455 –1.31 → –1.11 Na+/glucose cotransporter 
      Slc5a2 SPU_003667 –1.35 → +1.03 Na+/glucose transporter, low affinity 
      Slc5a12 SPU_018791 –1.39 → +1.07 Na+/glucose cotransporter 
      Slc2a5 SPU_027868 –1.31 → 1.00 Glucose/fructose transporter 
      Slc2a13 SPU_017752 –1.30 → +1.01 H+ myo-inositol symporter, glucose transport 
      Slc37a3 SPU_011768 –1.37 → +1.02 Glycerol-3-phosphate transporter 
      Slc16a12 SPU_004404 –1.33 → –1.08 Monocarboxylate transporter 
      Slc16a6 SPU_016408 –1.77 → +1.33 Monocarboxylate transporter 
      Slc16a4 SPU_009336 –1.53 → +1.17 Monocarboxylate transporter 
      Slc35a4 SPU_019603 –1.30 → 1.00 UDP-galactose transporter 
   Amino acid metabolism    
      amidase-like SPU_005666 –1.32 → –1.03 Amidase, hydrolase acting on C–N bonds 
      amidase-like SPU_002810 –1.59 → +1.18 Amidase, hydrolase acting on C–N bonds 
      amidase-like SPU_017354 –1.29 → –1.03 Amidase, hydrolase acting on C–N bonds 
      aulfite reductase SPU_019708 –1.55 → +1.14 Sulfite reductase, selenoamino acid metabolism 
      Slc7a9 SPU_021169 –1.45 → –1.18 Cationic amino acid transporter 
      Slc7a1 SPU_028697 –1.24 → –1.12 Cationic amino acid transporter 
      Slc7a6 SPU_004504 –1.25 → –1.09 Cationic amino acid transporter 
      Slc7a5 SPU_016082 –1.47 → +1.08 Cationic amino acid transporter, L-type 
      Slc43a3 SPU_002402 –1.33 → –1.06 FOAP-13, Na+-independent amino acid transporter 
      Slc36a1 SPU_022045 –1.43 → +1.06 Proton-coupled amino acid transporter 
      Slc15a2 SPU_012690 –1.25 → –1.08 H+/peptide transporter 
      Slc15a4 SPU_028146 –1.51 → +1.09 Peptide/histidine transporter 
      Slc7a11 SPU_007905 –1.41 → +1.05 Cystine/glutamate transporter 
      Slc32a1 SPU_025947 –1.35 → –1.01 GABA and glycine transporter 
      Dur3 SPU_011497 –1.49 → +1.08 Urea transporter 
      Slc3a1 SPU_013735 +1.30 → +1.04 Dibasic and neutral amino acid transport 
   Lipid metabolism    
      Acss1 SPU_018270 –1.38 → +1.03 Acyl-CoA synthetase, lipid biosynthesis 
      Slc5a7 SPU_020026 –1.36 → 1.00 Choline transporter, high affinity 
      Slc10a2 SPU_023059 –1.29 → –1.04 Na+ bile salt transporter 
      Slc10a1 SPU_003103 –1.38 → +1.06 Na+ bile salt transporter 
   Vitamin metabolism    
      Slc5a6 SPU_023702 –1.36 → –1.01 Na+-dependent vitamin transporter 
   Nucleotide metabolism    
      PRPS SPU_009841 –1.20 → –1.08 Phosphoribosyl pyrophosphate synthetase 
Protein synthesis – translational control    
   elF3j* SPU_013398 –1.48 → –1.32 Translation factor – initiation 
   elF2Bβ* SPU_004173 –1.40 → –1.20 Translation factor – initiation 
   elF5Bϵ SPU_015443 –1.28 → –1.04 Translation factor – initiation 
   elF4E-BP SPU_005957 –1.63 → +1.17 Translation factor – initiation 
   elF5B SPU_001393 –1.67 → 1.06 Translation factor – initiation 
   elF2Bα SPU_024859 –1.65 → 1.07 Translation factor – initiation 
   UPF3 SPU_000502 –1.32 → –1.07 Up-frameshift protein, translation factor – termination 
GeneGene IDFold change (FCUL → FCLL)Protein information
Acid–base and ion regulation    
   Slc8a3 SPU_026183 –1.52 → –1.02 Na+/Ca2+ exchanger 
   Slc41a1 SPU_001481 –1.35 → –1.13 mgtE-like Mg2+ transporter 
   Scnn1a SPU_014519 –1.43 → –1.07 Sodium channel 
   Aqp SPU_023979 –1.40 → –1.09 Aquaporin, water channel 
   Slc12a2 SPU_004877 –1.35 → –1.12 Na+/K+/2Cl cotransporter 
   Slco5a1 SPU_004407 –1.29 → –1.06 Organic anion transporter 
   Slc39a3 SPU_002226 –1.38 → –1.02 Zinc transporter 
   Slc24a4 SPU_023689 –1.37 → +1.03 Na+/K+/Ca2+ exchanger 
   Slco SPU_007603 –1.31 → –1.01 Organic anion transporter 
   Slc39a8 SPU_023011 –1.33 → +1.02 Zinc transporter 
   Atp13a4 SPU_005539 –1.26 → –1.03 H+/K+-ATPase 
   Slc20a2 SPU_020699 –1.30 → +1.02 Na-phosphate transporter, type III 
   Atp2a1 SPU_013051 –1.20 → –1.06 Ca2+-ATPase 
   Slc5a8 SPU_012573 –1.30 → –1.06 Na+-iodide related transporter 
   Slc5a5 SPU_021781 –1.36 → +1.02 Na+-iodide symporter 
   Aqp* SPU_021388 +1.46 → +1.07 Aquaporin, water channel and potentially CO2 
Apoptosis    
   Caspase 8-like2a SPU_008540 –1.27 → –1.04 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 8-like2b SPU_022177 –1.29 → 1.00 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 8-like3* SPU_016039 –1.28 → –1.18 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 8-like5 SPU_024371 –1.36 → +1.05 Cysteine protease, cell extrinsic pathway of apoptosis 
   Caspase 3/7-like SPU_002280 –1.33 → –1.05 Cysteine protease, last caspase in pathway before cell death 
   caspase N2a SPU_009497 –1.26 → –1.03 Cysteine protease, N for novel 
   caspase N2f SPU_026743 –1.32 → –1.01 Cysteine protease, N for novel 
   caspase N3a SPU_017523 –1.46 → +1.02 Cysteine protease, N for novel 
   caspase N6a SPU_006866 –1.37 → +1.02 Cysteine protease, N for novel 
   caspase N6b SPU_027596 –1.27 → –1.03 Cysteine protease, N for novel 
   ICE like-1a SPU_002921 –1.75 → +1.26 Interleukin-converting enzyme, cysteine protease 
   ICE like-2 SPU_021141 –1.28 → –1.08 Interleukin-converting enzyme, cysteine protease 
   ICE like-3 SPU_011872 –1.32 → –1.04 Interleukin-converting enzyme, cysteine protease 
   ICE like-4 SPU_012722 –1.34 → –1.08 Interleukin-converting enzyme, cysteine protease 
   Tnfsf-like3 SPU_015654 –1.32 → –1.02 Tumor necrosis factor subfamily like 3, ligand for TNFR with death domain 
   Tnfsf-like1 SPU_009528 –1.38 → +1.04 Tumor necrosis factor subfamily like 1, ligand for TNFR lacking death domain 
   Tnfrsf1a SPU_012211 –1.38 → +1.01 Tumor necrosis factor receptor (TNFR) superfamily 1, trigger apoptosis upon binding of Ligand (TNF) 
   Tnfrsf-like1 SPU_010230 –1.28 → –1.06 TNFR 
   Tnfrsf-cl1 SPU_010180 –1.36 → 1.00 TNFR, lacks death domain 
   HVEM/Eda2r-like 1 SPU_024584 –1.37 → +1.01 TNFR, lacks death domain 
   Troy/Eda2r-like 2 SPU_020740 –1.42 → +1.05 TNFR, lacks death domain 
   TRAF3 SPU_026495 –1.64 → +1.09 Tnf receptor-associated factor 3, adaptor without death domain 
   TRAF4 SPU_008332 –1.38 → –1.02 Adaptor without death domain 
   TRAF6 SPU_028898 –1.47 → +1.08 Adaptor without death domain 
   BIRC2b SPU_014057 –1.39 → –1.05 Baculoviral IAP repeat-containing 2, anti-apoptotic 
   BOK SPU_021416 –1.33 → –1.05 Bcl2-related ovarian killer, pro-apoptotic 
   IAP1 SPU_014350 –1.39 → +1.04 Inhibitor of apoptosis 1, anti-apoptotic 
   Mil2 SPU_001916 –1.40 → +1.05 Bcl-2 protein, pro-apoptotic 
   Slc22a13 SPU_017736 –1.35 → +1.02 Organic anion transporter, involved in apoptosis 
   Slc22a15 SPU_019637 –1.24 → –1.05 Organic anion transporter, involved in apoptosis 
Biomineralization    
   MSP130* SPU_013821 –1.42 → –1.05 Primary mesenchyme cell (PMC)-specific protein, cell surface 
   MSP130-related 6 SPU_014492 –1.31 → –1.02 PMC-specific protein 
   Runt-2 SPU_007852 –1.34 → –1.09 Transcription factor, triggers differentiation of skeletogenic cells 
   Alx1 SPU_022817 –1.37 → –1.05 PMC-specific protein, required for skeleton formation 
   serine rich protein 12 SPU_015338 –1.31 → –1.01 Glycoprotein that binds calcium 
   SPARC-like SPU_012548 –1.46→ +1.10 Secreted protein acidic and rich in cysteine, binds Ca2+ 
   Casr SPU_0017585 –1.26→ –1.04 Calcium receptor 
   CA-4 likeB SPU_022346 –1.38 → +1.04 Carbonic anhydrase, catalyzes reversible hydration of CO2 to bicarbonate and protons 
   CA-10 like SPU_0004135 –1.31→ 1.00 Carbonic anhydrase 
   CA-8 likeB SPU_026483 –1.23→ –1.06 Carbonic anhydrase 
   CA-12 likeB SPU_025722 –1.21→ –1.06 Carbonic anhydrase 
   CA-7 likeA SPU_012518 +1.55→ +1.03 Carbonic anhydrase, extracellular 
Cell cycle    
   Cdc23/Apc8 SPU_012696 –1.72 → –1.24 Cell division cycle 23, ubiquitin-proteolysis pathway 
   Slc29a4 SPU_008397 –1.47 → –1.10 Nucleoside transporter 
   Slc28a2 SPU_025779 –1.38 → –1.01 Na+-coupled nucleoside transporter 
   Apc11 SPU_021695 –1.28 → –1.07 Anaphase promoting complex 11, ubiquitin-proteolysis pathway 
   Myt1 SPU_008280 –1.32 → –1.04 Tyrosine kinase, inhibits cylin dependent kinase 1 
   PFAIRE SPU_003654 –1.46 → +1.07 Cyclin dependent kinase 
   Neka SPU_017790 –1.41 → +1.07 NIMA related kinase, mitotic kinase 
   SMC1 SPU_021629 +1.46 → +1.05 Structural maintenance of chromosome 1, condensin/cohesin complexes 
   SMC4* SPU_013617 +1.31 → 1.00 Structural maintenance of chromosome 4, condensin/cohesin complexes 
Cellular stress defensome    
   Protein homeostasis    
      Hsp100B SPU_006012 –1.44 → +1.04 100kDa heat shock protein, molecular chaperone 
      Hsp701B SPU_005808 –1.36 → +1.01 70kDa heat shock protein, molecular chaperone 
      Hsp701F SPU_013289 –1.26 → –1.04 70kDa heat shock protein, molecular chaperone 
      Hsp703A SPU_014864 –1.33 → 1.00 70kDa heat shock protein, molecular chaperone 
      Hsp70–like SPU_021458 –1.32 → +1.03 70kDa heat shock protein, molecular chaperone 
      Hsp20.1 SPU_001357 –1.19 → –1.12 20kDa heat shock protein, molecular chaperone 
      Hsp20.2 SPU_020294 –1.32 → 1.00 20kDa heat shock protein, molecular chaperone 
      UBXD1 SPU_012427 –1.33 → –1.02 UBX domain containing 1, Ub-proteasome pathway 
      ubiquitin SPU_015276 +1.38 → +1.15 Ubiquitin-proteasome pathway, signaling 
      Hsp40A* SPU_016562 +1.39 → +1.08 40kDa heat shock protein, co-chaperone of Hsp70 
   Antioxidant defense    
      Maf SPU_025888 –1.36 → –1.07 Transcription factor, oxidative stress-responsive 
      MGST-2 SPU_008286 –1.48 → +1.08 Glutathione S-transferase, microsomal 
      GST-12 SPU_023664 –1.32 → 1.00 Glutathione S-transferase, cytosolic 
      Gpx1 SPU_004397 –1.42 → +1.05 Glutathione peroxidase 7 
   Toxicant, metal and xenobiotic defense    
      Akr1a-like SPU_027986 –1.31 → –1.10 Aldo-keto reductase 
      Akr1b-like2 SPU_016996 –1.33 → –1.10 Aldo-keto reductase 
      Akr1b-like3 SPU_018466 –1.54 → +1.14 Aldo-keto reductase 
      Cyp2-like9* SPU_003606 –1.36 → –1.07 Cytochrome P450 monooxygenase, iron homeostasis 
      Cyp3-like8 SPU_016056 –1.38 → –1.01 Cytochrome P450 monooxygenase 
      Cyp4-like5 SPU_007558 –1.37 → +1.02 Cytochrome P450 monooxygenase 
      Cyp2-like14 SPU_006574 –1.21 → –1.08 Cytochrome P450 monooxygenase 
      Fmo5 SPU_022596 –1.26 → –1.08 Flavin-containing monooxygenase 5 
      Fmo3 SPU_022597 –1.35 → +1.02 Flavin-containing monooxygenase 3 
      ABCC9i SPU_018527 –1.39 → –1.02 ATP-binding cassette superfamily, efflux transporter 
      ABCG2 SPU_024785 –1.37 → 1.00 ATP-binding cassette superfamily, efflux transporter 
      Aldh3a1 SPU_009853 –1.32 → 1.00 Aldehyde dehydrogenase 
      Nat-like SPU_012976 –1.20 → –1.09 N-acyltransferase-like 
      NR1H6a SPU_017404 –1.31 → –1.09 Nuclear receptor subfamily 1 H member 6a 
      Ark1b-like4 SPU_028344 +1.46 → +1.05 Aldo-keto reductase 
      Fth1 SPU_004876 +1.52 → +1.07 Heavy chain of ferritin, iron storage 
      Fmo2 SPU_014947 +1.21 → +1.09 Flavin-containing monooxygenase 2 
   Adrenergic stress response    
      nAChR α7 SPU_013095 –1.37 → –1.01 Acetylcholine receptor, nicotinic 
      nAChR α9 SPU_005670 –1.36 → +1.00 Acetylcholine receptor, nicotinic 
      nAChR α4 SPU_019711 –1.56 → +1.17 Acetylcholine receptor, nicotinic 
      mAChR M5 SPU_016177 –1.45 → +1.07 Acetylcholine receptor, muscarinic 
      mAChR M4 SPU_019228 –1.30 → –1.02 Acetylcholine receptor, muscarinic 
      Slc22a3 SPU_006524 –1.39 → –1.04 Monoamine transporter, extraneuronal 
      Slc6a2 SPU_022506 –1.35 → +1.05 Sodium-dependent noradrenaline transporter 
      calcineurin SPU_018404 –1.25 → –1.08 Activates transcription of interleukin 2 
      SNAP-25 SPU_006859 –1.27 → –1.02 Synaptosome-associated protein 
Development    
   FoxB SPU_004551 –1.20 → –1.10 Forkhead box B, transcription factor 
   Trh SPU_014249 –1.29 → 1.00 Neuronal PAS domain protein 
   early-histone-H2a SPU_002577 +1.62 → +1.03 Involved in nucleosome assembly 
   FoxQ2 SPU_019002 +1.43 → +1.30 Forkhead box Q2, involved in axis specification 
   Not SPU_002129 +1.42 → +1.03 Transcription factor involved in differentiation 
   PKS-like* SPU_002895 +1.41 → +1.05 Polyketide synthase, pigment synthesis 
   Eve SPU_012253 +1.39 → +1.08 Even-skipped, body morphogenesis 
   Hes SPU_021608 +1.28 → +1.14 Hairy/enhancer of split, role in skeletogenic GRN 
   Otx SPU_010424 +1.40 → –1.04 Orthodenticle homeobox, role in endomesoderm GRN 
Kinome    
   FAK SPU_019686 –1.30 → –1.11 Focal adhesion kinase, cytoskeletal kinase 
   KIS SPU_027616 –1.32 → –1.09 Kinase interacting stathmin, cytoskeletal kinase 
   MLCKb SPU_000442 –1.37 → –1.04 Myosin light chain kinase, cytoskeletal kinase 
   projectin SPU_013917 –1.33 → –1.06 Cytoskeletal kinase 
   MAPKAPK5a SPU_013910 –1.24 → –1.14 Mitogen-activated protein kinase signaling 
   JAK2 SPU_020082 –1.47 → +1.06 Janus kinase 2, receptor signaling 
   JAK1 SPU_022495 –1.34 → –1.02 Janus kinase 1, receptor signaling 
   titin SPU_005613 –1.23 → –1.11 Cytoskeletal kinase 
   RIPK1-4A SPU_005215 –1.27 → –1.06 Receptor-interacting protein kinase, death kinase 
   LIMK SPU_022207 –1.56 → +1.17 LIM domain kinase, cytoskeletal kinase 
   ULK3 SPU_017980 –1.26 → –1.05 Unc-51-like kinase 3, cytoskeletal kinase 
Metabolism    
   Energy metabolism    
      Slc25a5* SPU_004813 –1.92 → –1.17 ADP, ATP carrier protein 2, energy transfer 
      Slc25a21 SPU_006682 –1.41 → +1.06 Mitochondrial oxodicarboxylate carrier, energy transfer 
      Atp5b SPU_005296 +1.51 → –1.01 ATP synthase, H+ transporting, F1 complex 
   Carbohydrate metabolism    
      glycosidase SPU_010831 –1.38 → –1.08 Glycosidase, degrades complex carbohydrates 
      β-d-xylosidase SPU_021638 –1.34 → 1.00 β-d-xylosidase, glycosidase 
      Ldh-d SPU_026206 –1.24 → –1.08 Lactate dehydrogenase d, anaerobic glycolysis 
      Mdh-1 SPU_023277 –1.33 → +1.05 Malate dehydrogenase 1, citric acid cycle 
      Pgm SPU_024573 –1.29 → –1.01 Phosphoglycerate mutase, glycolysis 
      Pgm2-like1 SPU_028876 –1.51 → +1.13 Phosphoglycerate mutase 2-like 1, glycolysis 
      Slc5a9 SPU_021455 –1.31 → –1.11 Na+/glucose cotransporter 
      Slc5a2 SPU_003667 –1.35 → +1.03 Na+/glucose transporter, low affinity 
      Slc5a12 SPU_018791 –1.39 → +1.07 Na+/glucose cotransporter 
      Slc2a5 SPU_027868 –1.31 → 1.00 Glucose/fructose transporter 
      Slc2a13 SPU_017752 –1.30 → +1.01 H+ myo-inositol symporter, glucose transport 
      Slc37a3 SPU_011768 –1.37 → +1.02 Glycerol-3-phosphate transporter 
      Slc16a12 SPU_004404 –1.33 → –1.08 Monocarboxylate transporter 
      Slc16a6 SPU_016408 –1.77 → +1.33 Monocarboxylate transporter 
      Slc16a4 SPU_009336 –1.53 → +1.17 Monocarboxylate transporter 
      Slc35a4 SPU_019603 –1.30 → 1.00 UDP-galactose transporter 
   Amino acid metabolism    
      amidase-like SPU_005666 –1.32 → –1.03 Amidase, hydrolase acting on C–N bonds 
      amidase-like SPU_002810 –1.59 → +1.18 Amidase, hydrolase acting on C–N bonds 
      amidase-like SPU_017354 –1.29 → –1.03 Amidase, hydrolase acting on C–N bonds 
      aulfite reductase SPU_019708 –1.55 → +1.14 Sulfite reductase, selenoamino acid metabolism 
      Slc7a9 SPU_021169 –1.45 → –1.18 Cationic amino acid transporter 
      Slc7a1 SPU_028697 –1.24 → –1.12 Cationic amino acid transporter 
      Slc7a6 SPU_004504 –1.25 → –1.09 Cationic amino acid transporter 
      Slc7a5 SPU_016082 –1.47 → +1.08 Cationic amino acid transporter, L-type 
      Slc43a3 SPU_002402 –1.33 → –1.06 FOAP-13, Na+-independent amino acid transporter 
      Slc36a1 SPU_022045 –1.43 → +1.06 Proton-coupled amino acid transporter 
      Slc15a2 SPU_012690 –1.25 → –1.08 H+/peptide transporter 
      Slc15a4 SPU_028146 –1.51 → +1.09 Peptide/histidine transporter 
      Slc7a11 SPU_007905 –1.41 → +1.05 Cystine/glutamate transporter 
      Slc32a1 SPU_025947 –1.35 → –1.01 GABA and glycine transporter 
      Dur3 SPU_011497 –1.49 → +1.08 Urea transporter 
      Slc3a1 SPU_013735 +1.30 → +1.04 Dibasic and neutral amino acid transport 
   Lipid metabolism    
      Acss1 SPU_018270 –1.38 → +1.03 Acyl-CoA synthetase, lipid biosynthesis 
      Slc5a7 SPU_020026 –1.36 → 1.00 Choline transporter, high affinity 
      Slc10a2 SPU_023059 –1.29 → –1.04 Na+ bile salt transporter 
      Slc10a1 SPU_003103 –1.38 → +1.06 Na+ bile salt transporter 
   Vitamin metabolism    
      Slc5a6 SPU_023702 –1.36 → –1.01 Na+-dependent vitamin transporter 
   Nucleotide metabolism    
      PRPS SPU_009841 –1.20 → –1.08 Phosphoribosyl pyrophosphate synthetase 
Protein synthesis – translational control    
   elF3j* SPU_013398 –1.48 → –1.32 Translation factor – initiation 
   elF2Bβ* SPU_004173 –1.40 → –1.20 Translation factor – initiation 
   elF5Bϵ SPU_015443 –1.28 → –1.04 Translation factor – initiation 
   elF4E-BP SPU_005957 –1.63 → +1.17 Translation factor – initiation 
   elF5B SPU_001393 –1.67 → 1.06 Translation factor – initiation 
   elF2Bα SPU_024859 –1.65 → 1.07 Translation factor – initiation 
   UPF3 SPU_000502 –1.32 → –1.07 Up-frameshift protein, translation factor – termination 

Data are presented as the upper (FCUL) and lower (FCLL) limits of fold change

*

Genes that were also within the group of mRNA transcripts that changed significantly in response to Moderate CO2 conditions

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