Document downloaded from http://www.elsevier.es, day 24/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Table S1. Complete gene list. GenBank RefSeq and description of each gene were provided by the array supplier. Unigene GeneBank Symbol Description Gene Name/s Rn.11422 NM_033230 Akt1 V-akt murine thymoma viral oncogene homolog 1 Akt Rn.2104 NM_019288 App Amyloid beta (A4) precursor protein - Rn.23323 NM_001034933 Arsa Arylsulfatase A MGC125207 Rn.94004 NM_033443 Arsb Arylsulfatase B - Rn.6224 NM_001038495 Atg12 ATG12 autophagy related 12 Apg12l, MGC125080 Rn.101734NM_001108809 Atg16l1 ATG16 autophagy related 16-like 1 Apg16l, Wdr30 Rn.104199NM_001191560 Atg16l2 ATG16 autophagy related 16-like 2 RGD1311400 Rn.3084 NM_134394 Atg3 ATG3 autophagy related 3 Apg3l, PIG-1, Pig1 Rn.163086NM_001025711 Atg4b ATG4 autophagy related 4 homolog B Apg4b, MGC112887 Rn.23378 NM_001107948 Atg4c ATG4 autophagy related 4 homolog C - Rn.98385 NM_001014250 Atg5 ATG5 autophagy related 5 - Rn.162765NM_001012097 Atg7 ATG7 autophagy related 7 Apg7l Rn.35248 NM_001014218 Atg9a ATG9 autophagy related 9 homolog A MGC105908, RGD1310450 Rn.36696 NM_022698 Bad BCL2-associated agonist of cell death MGC72439 Rn.14598 NM_053812 Bak1 BCL2-antagonist/killer 1 MGC108627 Rn.10668 NM_017059 Bax Bcl2-associated X protein - Rn.9996 NM_016993 Bcl2 B-cell CLL/lymphoma 2 Bcl-2 Rn.10323 NM_031535 Bcl2l1 Bcl2-like 1 Bcl-xl, Bcl2l, Bclx, bcl-X Rn.2776 NM_053739 Becn1 Beclin 1, autophagy related - Rn.31142 NM_022684 Bid BH3 interacting domain death agonist - Rn.2060 NM_053420 Bnip3 BCL2/adenovirus E1B interacting protein 3 MGC93043 Rn.10562 NM_012922 Casp3 Caspase 3 Lice, MGC93645 Rn.54474 NM_022277 Casp8 Caspase 8 - Rn.29897 NM_031762 Cdkn1b Cyclin-dependent kinase inhibitor 1B CDKN4, Cdki1b, Kip1, P27KIP1, p27 Rn.48717 NM_031550 Cdkn2a Cyclin-dependent kinase inhibitor 2A Arf, INK4A, MTS1, p16, p16Cdkn2a, p19ARF Rn.102386NM_001006971 Cln3 Ceroid-lipofuscinosis, neuronal 3 MGC94583 Rn.100909 NM_022597 Ctsb Cathepsin B - Rn.11085 NM_134334 Ctsd Cathepsin D - Rn.11347 NM_017320 Ctss Cathepsin S - Rn.44431 NM_022205 Cxcr4 Chemokine (C-X-C motif) receptor 4 MGC108696 Rn.23108 NM_001107335 Dapk1 Death associated protein kinase 1 - Rn.24897 NM_031599 Eif2ak3 Eukaryotic translation initiation factor 2 alpha kinase PEK 3 Rn.101803 XM_213569 Eif4g1 Eukaryotic translation initiation factor 4 gamma, 1 - Rn.10595 NM_012689 Esr1 Estrogen receptor 1 ER-alpha, Esr, RNESTROR Rn.16183 NM_152937 Fadd Fas (TNFRSF6)-associated via death domain Mort1 Rn.162521 NM_139194 Fas Fas (TNF receptor superfamily, member 6) Tnfrsf6 Rn.162368 NM_199118 Gaa Glucosidase, alpha, acid MGC72625 Rn.8411 NM_172036 Gabarap GABA(A) receptor-associated protein - Rn.64537 NM_022706 Gabarapl2 GABA(A) receptor-associated protein like 2 Gef2, MGC108686 Rn.1863 NM_001025409 Hdac1 Histone deacetylase 1 - Rn.13453 XM_228753 Hdac6 Histone deacetylase 6 - Rn.21 NM_019387 Hgs Hepatocyte growth factor-regulated tyrosine kinase Hrs substrate Rn.119867 NM_175761 Hsp90aa1 Heat shock protein 90, alpha (cytosolic), class A Hsp86, Hsp90, Hspca, member 1 MGC105293 Rn.120392 NM_024351 Hspa8 Heat shock protein 8 Hsc70, MGC114311 Rn.11193 NM_024357 Htt Huntingtin Hd, Hdh N/A XM_233152 Ifna2 Interferon alpha family, gene 2 - Rn.218577NM_001106667 Ifna4 Interferon, alpha 4 - Rn.10795 NM_138880 Ifng Interferon gamma IFNG2 Rn.6282 NM_178866 Igf1 Insulin-like growth factor 1 - Rn.989 NM_019130 Ins2 Insulin 2 - Rn.20356 NM_001012007 Irgm Immunity-related GTPase family, M Ifi1 Rn.40177 NM_012857 Lamp1 Lysosomal-associated membrane protein 1 LGP120 Rn.3135 NM_199500 Map1lc3a Microtubule-associated protein 1 light chain 3 alpha MGC105263 Rn.41412 NM_022867 Map1lc3b Microtubule-associated protein 1 light chain 3 beta MGC93422, Map1lc3, Mpl3, zbs559 Rn.88085 NM_031020 Mapk14 Mitogen activated protein kinase 14 CRK1, CSBP, CSPB1, Csbp1, Csbp2, Exip, Hog, MGC105413, Mxi2, Prkm14, Prkm15, RK, Sapk2A, p38, p38Hog, p38alpha Document downloaded from http://www.elsevier.es, day 24/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Rn.4090 XM_341399 Mapk8 Mitogen-activated protein kinase 8 JNK Rn.2411 XM_342346 Nfkb1 Nuclear factor of kappa light polypeptide gene NF-kB enhancer in B-cells 1 Rn.133954NM_001134341 Ambra1 Autophagy/beclin 1 regulator 1 Nyw1 Rn.30010 NM_022958 Pik3c3 Phosphoinositide-3-kinase, class 3 - Rn.152697NM_001106723 Pik3cg Phosphoinositide-3-kinase, catalytic, gamma Pi3k polypeptide Rn.8917 NM_001108777 Pik3r4 Phosphoinositide-3-kinase, regulatory subunit 4 - Rn.87789 NM_019142 Prkaa1 Protein kinase, AMP-activated, alpha 1 catalytic 5'-AMP- subunit activatedproteinkinasealpha- 1catalyticsubunit, 5-AMP- activatedproteinkinasealpha- 1catalyticsubunit Rn.64583 NM_023991 Prkaa2 Protein kinase, AMP-activated, alpha 2 catalytic AMPK subunit Rn.44440 NM_019163 Psen1 Presenilin 1 - Rn.22158 NM_031606 Pten Phosphatase and tensin homolog MMAC1, Mmac, TEP1 Rn.6295 NM_001015023 Rab24 RAB24, member RAS oncogene family MGC108835 Rn.55115 NM_017045 Rb1 Retinoblastoma 1 - Rn.33137 NM_001107901 Rb1cc1 RB1-inducible coiled-coil 1 - Rn.4038 NM_001007659 RGD1359310 Similar to RIKEN cDNA 9430023L20 Atg101, MGC94201 Rn.88166 NM_021661 Rgs19 Regulator of G-protein signaling 19 Camki, Gaip, MGC108699 Rn.4042 NM_031985 Rps6kb1 Ribosomal protein S6 kinase, polypeptide 1 - Rn.1827 NM_019169 Snca Synuclein, alpha (non A4 component of amyloid MGC105443 precursor) Rn.107103 NM_181550 Sqstm1 Sequestosome 1 Osi, ZIP, ZIP3 Rn.40136 NM_021578 Tgfb1 Transforming growth factor, beta 1 - Rn.10 NM_019386 Tgm2 Transglutaminase 2, C polypeptide TgaseII Rn.12071 NM_001012155 Tm9sf1 Transmembrane 9 superfamily member 1 - Rn.1279 NM_001025018 Dram2 DNA-damage regulated autophagy modulator 2 MGC109061, Tmem77 Rn.2275 NM_012675 Tnf Tumor necrosis factor (TNF superfamily, member 2) MGC124630, RATTNF, TNF-alpha, Tnfa Rn.83627 NM_145681 Tnfsf10 Tumor necrosis factor (ligand) superfamily, member Trail 10 Rn.54443 NM_030989 Tp53 Tumor protein p53 MGC112612, Trp53, p53 Rn.103860NM_001108696 Tp73 Tumor protein p73 P73, Trp73 Rn.24509 NM_001108341 Ulk1 Unc-51 like kinase 1 (C. elegans) - Rn.99218 NM_001107536 Uvrag UV radiation resistance associated gene - Rn.203725NM_001127297 Wipi1 WD repeat domain, phosphoinositide interacting 1 RGD1307754 Rn.973 NM_001007604 Rplp1 Ribosomal protein, large, P1 MGC72935 Rn.47 NM_012583 Hprt1 Hypoxanthine phosphoribosyltransferase 1 Hgprtase, Hprt, MGC112554 Rn.92211 NM_173340 Rpl13a Ribosomal protein L13A - H05 Rn.94978 NM_031144 Actb Actin, beta Rn.107896 NM_017025 Ldha Lactate dehydrogenase A Ldh1 Document downloaded from http://www.elsevier.es, day 24/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Table S2. Array components. Functional gene grouping. Autophagy Machinery Components: Components Involved in Autophagic Vacuole Formation: AMBRA1, ATG12, ATG16L1, ATG4A, ATG4B, ATG4C, ATG4D, ATG5, ATG9A, ATG9B, BECN1, GABARAP, GABARAPL1, GABARAPL2, IRGM, MAP1LC3A, MAP1LC3B, RGS19, ULK1. Components Responsible for Protein Targeting to Membrane / Vacuole: ATG4A, ATG4B, ATG4C, ATG4D, GABARAP. Components Responsible for Protein Transport: ATG10, ATG16L1, ATG16L2, ATG3, ATG4A, ATG4B, ATG4C, ATG4D, ATG7, ATG9A, GABARAP, GABARAPL2, RAB24. Components Linking Autophagosome to Lysosome: DRAM1, GABARAP, FAM176A. Components Involved in Protein Ubiquitination: ATG3, ATG7. Components with Protease Activity: ATG4A, ATG4B, ATG4C, ATG4D. Regulation of Autophagy: Co-Regulators of Autophagy and Apoptosis: AKT1, APP, ATG12, ATG5, BAD, BAK1, BAX, BCL2, BCL2L1, BECN1, BID, BNIP3, CASP3, CASP8, CDKN1B, CDKN2A, CLN3, CTSB, CXCR4, DAPK1, DRAM1, EIF2AK3, FADD, FAS, HDAC1, HTT, IFNA2, IFNG, IGF1, INS, MAPK8, NFKB1, PIK3CG, PRKAA1, PTEN, SNCA, SQSTM1, TGFB1, TGM2, TNF, TNFSF10, TP53, TP73. Co-Regulators of Autophagy and the Cell Cycle: BAX, CDKN1B, CDKN2A, IFNG, PTEN, RB1, TGFB1, TP53, TP73. Autophagy Induction by Intracellular Pathogens: EIF2AK3, IFNA2, IFNA4, IFNG. Autophagy in Response to Other Intracellular Signals: ARSA, CTSS, EIF4G1, ESR1, GAA, HGS, MAPK14, PIK3C3, PIK3R4, PRKAA2, RPS6KB1, TMEM74, DRAM2, ULK2, UVRAG. Chaperone-Mediated Autophagy: HSP90AA1, HSPA8. Document downloadedfromhttp://www.elsevier.es,day24/09/2021.Thiscopyisforpersonaluse.Anytransmissionofthisdocumentbyanymediaorformatstrictlyprohibited. Tables S3-S4. Supplementary gene expression data associated with this article. Gene expression after infections with L. monocytogenes in rat brain organotypic cultures at different time points (5 h and 12 h respectively). Table S3 AVG Ct Standard Deviation 2^(-Avg.(Delta(Ct)) Up-Down Regulation (comparing to control group) p-value (comparing to Symbol Description Control Infected Control Infected Control Infected Fold Regulation control group) Akt1 V-akt murine thymoma viral oncogene homolog 1 30.23 30.75 0.269162 0.928754 0.017726 0.009685 0.207264 -1.8302 App Amyloid beta (A4) precursor protein 23.88 23.98 0.216028 0.373154 1.445932 1.060688 0.100173 -1.3632 Arsa Arylsulfatase A 30.87 31.35 0.252602 1.045118 0.011375 0.006412 0.192415 -1.774 Arsb Arylsulfatase B 28.11 28.22 0.23231 0.528568 0.077053 0.055939 0.244029 -1.3775 Atg12 ATG12 autophagy related 12 28.71 29.43 0.345526 0.75923 0.050836 0.024265 0.033417 -2.0951 Atg16l1 ATG16 autophagy related 16-like 1 29.87 30.23 0.39689 0.704157 0.022697 0.013888 0.156155 -1.6343 Atg16l2 ATG16 autophagy