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1 Supplemental Informations Microarray Method Total RNA Was Supplemental Informations Microarray method Total RNA was purified using nucleospin RNA L columns (Macherey Nagel, Hoerdt, France) according to the manufacturer’s recommendations. cDNA synthesis and biotin labelling of cRNA were performed using 5 µg total RNA and according to One-Cycle Target Labelling protocol (Affymetrix, Santa Clara, CA). cRNA were hybridized to 12 Mouse Genome 430A GeneChips (1 mouse per chip) and analyzed using a GeneChip 3000 7G scanner and the GeneChip Operative Software v1.1.1 (Affymetrix) at the Gene Expression core facility of the Institute for Biotherapy (Montpellier, France). CEL files were processed using the ChipInspector software (Genomatix, Munich, Germany). ChipInspector uses single probe expression levels as input and map to transcripts probes that uniquely display significant changes. The methods circumvent false negative resulting from low signal probes, annotation errors and errors due to the existence of alternative transcripts. Differentially expressed genes between the AL and MT groups at both time points were identified using a SAM (Significance analysis of Microarrays) one class comparison with the following settings: false discovery rate of 0.5%; minimal probe coverage: 3; minimal fold change threshold of 1.5. Down and up-regulated genes from both datasets (CT4 and CT16) were mapped to the Gene Ontology (GO) biological process terms and calculated as over- represented (z-score) relative to the expected number of regulated genes in each GO category. Cluster 3.0 and Treeview were used to construct the heatmap of the subset of genes regulated in a time dependent manner in the tumor of mice with restricted access to food. Legends to figures Supplementary Figure S1: Mean body weight in pooled Exp I and Exp II on the day preceding tumor inoculation (A) or 21 days after tumor inoculation (B) in mice fed ad libitum 1 (AL) or on meal timing (MT), with normal diet (N) or fat diet (F). Supplementary Figure S2: Plasma corticosterone and IGF rhythms 3 weeks after tumor inoculation in mice fed AL (dashed line) or on MT (solid line) with normal (left panels) or fat diet (right panels). Plasma corticosterone (upper row) and IGF (low row). Horizontal axis hatched and black rectangles indicate subjective light and dark spans of photoperiodic cycle, respectively. 2 Supplementary Tables Table S1: Biological processes down-regulated by meal timing at CT4 in P03 tumors. GO Term GO ID Total Observed Expected ZScore regulation of progression through cell cycle GO:0000074 361 11 1,05 9,87 response to unfolded protein GO:0006986 59 4 0,17 9,3 protein folding GO:0006457 185 7 0,54 8,9 cell cycle GO:0007049 642 12 1,86 7,61 mitosis GO:0007067 140 5 0,41 7,26 cell division GO:0051301 203 6 0,59 7,12 response to stress GO:0006950 711 9 2,06 4,96 response to biotic stimulus GO:0009607 204 4 0,59 4,47 regulation of transcription from RNA polymerase II promoter GO:0006357 348 4 1,01 3,02 metabolic process GO:0008152 5978 27 17,31 3 Table S2: Biological processes up-regulated by meal timing at CT4 in P03 tumors. GO Term GO ID Total Observed Expected ZScore mitosis GO:0007067 140 5 0,36 7,79 cytoskeleton organization and biogenesis GO:0007010 459 5 1,18 3,58 response to chemical stimulus GO:0042221 323 4 0,83 3,53 cell cycle GO:0007049 642 6 1,65 3,47 carbohydrate metabolic process GO:0005975 337 4 0,86 3,41 Table S3: Biological processes down-regulated by meal timing at CT16 in P03 tumors. GO Term GO ID Total Observed Expected ZScore response to heat GO:0009408 25 4 0,13 10,7 response to unfolded protein GO:0006986 59 5 0,31 8,45 response to protein stimulus GO:0051789 59 5 0,31 8,45 response to temperature stimulus GO:0009266 41 4 0,22 8,18 myeloid cell differentiation GO:0030099 96 6 0,51 7,77 protein folding GO:0006457 185 8 0,97 7,18 immune system development GO:0002520 242 8 1,27 6,02 hemopoietic or lymphoid organ development GO:0048534 227 7 1,19 5,36 response to chemical stimulus GO:0042221 323 8 1,7 4,9 response to biotic stimulus GO:0009607 204 6 1,07 4,8 hemopoiesis GO:0030097 204 6 1,07 4,8 developmental process GO:0032502 2560 27 13,48 4,05 organ development GO:0048513 1215 16 6,4 3,97 response to stress GO:0006950 711 11 3,74 3,85 response to abiotic stimulus GO:0009628 141 4 0,74 3,81 anatomical structure development GO:0048856 1752 20 9,22 3,78 cell differentiation GO:0030154 1534 18 8,08 3,69 RNA splicing GO:0008380 147 4 0,77 3,69 immune system process GO:0002376 646 10 3,4 3,67 regulation of apoptosis GO:0042981 411 7 2,16 3,34 metabolic process GO:0008152 5978 45 31,47 3,1 anatomical structure morphogenesis GO:0009653 999 12 5,26 3,05 system development GO:0048731 1500 16 7,9 3,05 RNA metabolic process GO:0016070 1899 19 10 3,05 protein targeting GO:0006605 190 4 1 3,03 embryonic development GO:0009790 362 6 1,91 3,01 3 Table S4: Biological processes up-regulated by meal timing at CT16 in P03 tumors. GO Term GO ID Total Observed Expected ZScore mitosis GO:0007067 140 14 1,57 10,04 cell cycle GO:0007049 642 26 7,18 7,22 cytokinesis GO:0000910 28 4 0,31 6,63 immune system process GO:0002376 646 23 7,23 6,03 immune response GO:0006955 410 16 4,59 5,43 taxis GO:0042330 106 6 1,19 4,46 nucleosome assembly GO:0006334 53 4 0,59 4,46 chemotaxis GO:0006935 106 6 1,19 4,46 protein-DNA complex assembly GO:0065004 86 5 0,96 4,15 biopolymer metabolic process GO:0043283 3453 61 38,63 4,12 skeletal development GO:0001501 159 7 1,78 3,96 microtubule cytoskeleton organization and biogenesis GO:0000226 64 4 0,72 3,91 bone remodeling GO:0046849 95 5 1,06 3,85 microtubule-based process GO:0007017 168 7 1,88 3,78 chromatin assembly GO:0031497 67 4 0,75 3,78 response to external stimulus GO:0009605 438 13 4,9 3,73 cell activation GO:0001775 216 8 2,42 3,64 tissue remodeling GO:0048771 104 5 1,16 3,59 regulation of cellular process GO:0050794 2956 51 33,07 3,49 leukocyte activation GO:0045321 200 7 2,24 3,22 protein modification GO:0006464 1223 25 13,68 3,21 hemopoiesis GO:0030097 204 7 2,28 3,16 ossification GO:0001503 85 4 0,95 3,15 biomineral formation GO:0031214 86 4 0,96 3,12 microtubule-based movement GO:0007018 88 4 0,98 3,07 leukocyte differentiation GO:0002521 127 5 1,42 3,03 cellular developmental process GO:0048869 1534 29 17,16 3,03 cell differentiation GO:0030154 1534 29 17,16 3,03 biopolymer modification GO:0043412 1266 25 14,16 3,02 regulation of cell growth GO:0001558 90 4 1,01 3,01 4 Table S5: Genes down-regulated in P03 tumors at CT4 after meal timing. Biological Process Symbol Gene name Coverage Fold change Cell cycle Pycard PYD and CARD domain containing 8 0.50 Cdkn2d cyclin-dependent kinase inhibitor 2D (p19) 3 0.60 Cdca3 cell division cycle associated 3/tome-1 4 0.62 Ccng2 cyclin G2 11 0.62 Ccnb1 cyclin B1 8 0.62 Aurkb aurora kinase B 3 0.62 Tacc3 transforming. acidic coiled-coil containing protein 3 3 0.62 Cdc20 cell division cycle 20 5 0.62 Plk1 polo-like kinase 1 4 0.63 Ccna2 cyclin A2 6 0.64 Aspm asp (abnormal spindle)-like. microcephaly associated 5 0.65 Racgap1 Rac GTPase-activating protein 1 5 0.65 Cell organization Prg4 proteoglycan 4 5 0,52 Kif23 kinesin family member 23 7 0.58 Kif22 kinesin family member 22 5 0.61 Nusap1 nucleolar and spindle associated protein 1 5 0.61 Cenpa centromere protein A 7 0.61 Cenpf centromere protein F 8 0.62 Kif11 kinesin family member 11 10 0.62 Cell communication Xlkd1 extra cellular link domain-containing 1 9 0.52 Efemp1 epidermal growth factor-containing fibulin-like extracellular 5 0.52 matrix protein 1 Differentiation Hoxc8 homeobox C8 3 0.57 Bmp4 bone morphogenetic protein 4 3 0.59 Iqgap3 Q motif containing GTPase activating protein 3 5 0.61 Metabolism Adipoq adiponectin 6 0.40 Cbr2 carbonyl reductase 2 4 0.48 Lpl lipoprotein lipase 6 0.58 Hnrpdl heterogeneous nuclear ribonucleoprotein D-like 10 0,61 Syncrip synaptotagmin binding, cytoplasmic RNA 4 0,61 Pdk1 pyruvate dehydrogenase kinase. isoenzyme 1 8 0.64 Acsl1 acyl-CoA synthetase long-chain family member 1 3 0.66 Immune system Ccl6 chemokine (C-C motif) ligand 6 12 0,47 Ccl8 chemokine (C-C motif) ligand 7 0,47 Cd5l CD5 antigen-like 7 0,50 Spib Spi-B transcription factor (Spi-1/PU.1 related) 3 0,56 Bcl6 B-cell leukemia/lymphoma 6 3 0,66 Stress response Alas2 aminolevulinic acid synthase 2 5 0.46 Cirbp cold inducible RNA binding protein 9 0.54 Lrmp lymphoid-restricted membrane protein 4 0.56 Zfp292 zinc finger protein 292 4 0.61 Signal transduction Sorbs3 sorbin and SH3 domain containing 3 3 0.53 Gpr133 G protein-coupled receptor 133 3 0.62 Transcription Klf6 Kruppel-like factor 6 9 0.63 Mxd3 Max dimerization protein 3 6 0.66 Others Kctd14 potassium channel tetramerisation domain containing 14 3 0,50 Mrc1 mannose receptor, C type 1 3 0,53 Marco macrophage receptor with collagenous structure 3 0,56 Mgl1 macrophage galactose N-acetyl-galactosamine specific lectin 1 4 0,56 Folr2 folate receptor 2 (fetal) 3 0,57 Crym crystallin, mu 5 0,58 C79407 expressed sequence C79407 3 0.61 6720460F02Rik 4 0.62 March7 membrane-associated ring finger (C3HC4) 7 4 0,65 Shcbp1 Shc SH2-domain binding protein 1 4 0.65 5 Table S6: Genes up-regulated in P03 tumors at CT4 after meal timing.
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