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Suppl. Fig. Legends Supplementary Figures. Supplementary Figure 1. Extent of lesions. a. Extent of smallest (dark gray), average (medium gray), and largest (light gray) lesions in animals treated as indicated 4 weeks after the induction of focal ischemia. b, Quantitation of lesion volume shows that neither treatment alters stroke volume (controls are shown for comparison and are from concurrently run animals reported in ref. 24). Supplementary Figure 2. Combinatorial treatment promotes axon rewiring on the intact side of the spinal cord. a. Low-power camera lucida drawing showing area in the cervical spinal cord contralateral to the undamaged hemisphere with BDA-labeled axon in close proximity to a ventral horn motorneuron in lamina IX. b, c. Photomicrograph (b) and camera lucida drawing (c) of labeled axon shown in a. Quantitation of BDA-labeled axons in lamina IX per mm in the cervical enlargement. *: Differences between groups significant at P < 0.05. Supplementary Figure 3. Sequence homology between the scrambled NEP1-40 peptide and myelin-associated glycoprotein (MAG). Top: Sequence of NEP1-40 and the scrambled peptide. Bottom: Alignment of the scrambled peptide and a region of MAG sharing 12/32 (37%) identities, and 17/32 (53%) positives. Gaps = 8/32 (25%). The probability of this similarity occurring by chance is estimated as 7 x 10-4 (PSI-BlastP of Scrambled NEP vs mouse NR databank at NCBI Blast). Zai et al., Suppl. Fig. 2 Supplementary Table 1 Stereotaxic coordinates for BDA injections Injection site Rostro-caudal Medio-lateral 1 0.12 -0.23 2 0.07 -0.18 3 0.02 -0.18 4 0.02 -0.39 5 -0.03 -0.29 6 -0.03 -0.15 7 -0.03 -0.41 8 -0.08 -0.23 9 -0.08 -0.31 10 -0.13 -0.25 11 -0.13 -0.33 12 -0.18 -0.23 13 -0.18 -0.31 14 -0.23 -0.23 15 -0.23 -0.31 16 -0.28 -0.25 17 -0.28 -0.33 18 -0.33 -0.31 Figures are in cm relative to Bregma Supplementary Table 2. Gene changes ≥ 1.7-fold, P < 0.01 a. Inosine vs. Saline, rats reared in isolation Transcript Symbol Definition fold-change XM_579393.1 LOC497757 hypothetical gene supported by NM_017090 (LOC497757). 11.19 XM_576562.1 LOC501140 similar to BCL2/adenovirus E1B 19 kDa-interacting protein 3 (LOC501140). 8.53 NM_053372.1 Slpi secretory leukocyte peptidase inhibitor (Slpi). 6.90 NM_053420.2 Bnip3 BCL2/adenovirus E1B 19 kDa-interacting protein 3 (Bnip3). 5.25 XM_574598.1 LOC499300 similar to protein tyrosine phosphatase, receptor type, C polypeptide-associated protein (LOC499300). 2.38 XM_579226.1 RT1-Ba RT1 class II, locus Ba (RT1-Ba). 2.22 XM_232418.3 Cd69 CD69 antigen (Cd69). 2.06 XM_226694.3 Zcchc9 zinc finger, CCHC domain containing 9 (Zcchc9). 2.05 NM_021838.2 Nos3 nitric oxide synthase 3, endothelial cell (Nos3). 2.05 NM_022268.1 Pygl liver glycogen phosphorylase (Pygl). 1.92 XM_223843.3 Rarb retinoic acid receptor, beta (Rarb). 1.87 XM_214585.2 LOC291675 similar to RIKEN cDNA 2010001M09 (LOC291675). 1.84 XM_217268.2 LOC301016 similar to Esophagus cancer-related gene-2 protein precursor (ECRG-2) (LOC301016). 1.77 NM_013069.1 Cd74 CD74 antigen (invariant polpypeptide of major histocompatibility class II antigen-associated) (Cd74). 1.76 NM_013169.1 Cd3d CD3 antigen delta polypeptide (Cd3d). 1.74 NM_078617.2 Rps23 ribosomal protein S23 (Rps23). 1.72 XM_340822.2 Per1 period homolog 1 (Drosophila) (Per1). 0.59 XM_215901.3 RGD1311066 similar to RIKEN cDNA 0610011L14 gene (RGD1311066). 0.58 NM_031678.1 Per2 period homolog 2 (Drosophila) (Per2). 0.56 NM_145775.1 Nr1d1 nuclear receptor subfamily 1, group D, member 1 (Nr1d1). 0.56 XM_575108.1 LOC499772 similar to immediate early response 5-like (LOC499772). 0.55 b. Inosine vs. Saline, rats reared in EE Transcript Symbol Definition fold-change XM_343479.2 Sema3b sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B (Sema3b). 6.61 NM_053394.1 Klf5 Kruppel-like factor 5 (Klf5). 5.32 NM_012792.1 Fmo1 flavin containing monooxygenase 1 (Fmo1). 5.19 XM_579512.1 Tagln transgelin (Tagln). 5.08 NM_017224.1 Slc22a6 solute carrier family 22 (organic anion transporter), member 6 (Slc22a6). 4.97 NM_199370.1 Krt2-8 keratin complex 2, basic, gene 8 (Krt2-8). 4.72 NM_052983.1 Slc5a5 solute carrier family 5 (sodium iodide symporter), member 5 (Slc5a5). 4.42 NM_001008767.1Txnip upregulated by 1,25-dihydroxyvitamin D-3 (Txnip). 4.22 NM_019156.1 Vtn vitronectin (Vtn). 4.21 NM_133623.1 Slc6a13 solute carrier family 6 (neurotransmitter transporter, GABA), member 13 (Slc6a13). 4.14 XM_216552.3 Tcea3 transcription elongation factor A (SII), 3 (Tcea3). 3.98 XM_238167.3 LOC293860 similar to Filamin A (Alpha-filamin) (Filamin 1) (Endothelial actin-binding protein) (Actin-binding protein 280) 3.86 NM_019363.2 Aox1 aldehyde oxidase 1 (Aox1). 3.84 NM_012811.1 Mfge8 milk fat globule-EGF factor 8 protein (Mfge8). 3.59 NM_012974.1 Lamb2 laminin, beta 2 (Lamb2). 3.48 NM_053857.1 Eif4ebp1 eukaryotic translation initiation factor 4E binding protein 1 (Eif4ebp1). 3.45 XM_341349.2 LOC361066 similar to 9930012K11Rik protein (LOC361066). 3.43 NM_138826.2 Mt1a Metallothionein (Mt1a). 3.39 NM_022500.2 Ftl1 ferritin light chain 1 (Ftl1). 3.28 NM_031834.1 Sult1a1 sulfotransferase family 1A, phenol-preferring, member 1 (Sult1a1). 3.21 NM_030859.1 Mdk midkine (Mdk). 3.05 XM_238327.3 Prrx2 paired related homeobox 2 (Prrx2). 3.01 NM_138828.1 Apoe apolipoprotein E (Apoe). 2.86 XM_579964.1 LOC499410 LOC499410 (LOC499410). 2.85 XM_573916.1 Pdgfrl platelet-derived growth factor receptor-like (Pdgfrl). 2.64 XM_579547.1 LOC497685 hypothetical gene supported by NM_032416 (LOC497685). 2.61 XM_216142.3 Rarres2 retinoic acid receptor responder (tazarotene induced) 2 (Rarres2). 2.54 NM_022504.1 Rpl36 ribosomal protein L36 (Rpl36). 2.54 NM_145776.1 Slc38a3 solute carrier family 38, member 3 (Slc38a3). 2.51 NM_172038.1 Gstm5 glutathione S-transferase, mu 5 (Gstm5). 2.39 XM_344403.2 Abhd4 abhydrolase domain containing 4 (Abhd4). 2.37 XM_212875.2 LOC293291 similar to ribosomal protein L36 (LOC293291). 2.33 NM_053578.3 Atp6v0e1 ATPase, H+ transporting, V0 subunit E isoform 1 (Atp6v0e1). 2.30 XM_340905.2 LOC360630 similar to Naglu (LOC360630). 2.25 XM_579319.1 RGD1306222 similar to 1810034B16Rik protein (RGD1306222). 2.25 XM_574353.1 LOC365179 similar to zinc finger protein 524 (LOC365179). 2.24 NM_199499.1 Lgi4 leucine-rich repeat LGI family, member 4 (Lgi4). 2.22 NM_001008520.1Abhd1 abhydrolase domain containing 1 (Abhd1). 2.20 NM_001009706.1MGC95092 similar to phospholysine phosphohistidine inorganic pyrophosphate phosphata (5M590) (MGC95092). 2.18 NM_012592.1 Ivd isovaleryl coenzyme A dehydrogenase (Ivd). 2.18 NM_053968.2 Mt3 metallothionein 3 (Mt3). 2.18 NM_001007664.1MGC93766 similar to RIKEN cDNA 1810013B01 (MGC93766). 2.16 NM_031756.1 Ggcx gamma-glutamyl carboxylase (Ggcx). 2.15 NM_031318.1 Tctex1 t-complex testis expressed 1 (Tctex1). 2.10 XM_220805.3 Appbp2 amyloid beta precursor protein (cytoplasmic tail) binding protein 2 (Appbp2). 2.03 XM_214321.3 Bpy2ip1 BPY2 interacting protein 1 (Bpy2ip1). 2.01 XM_341095.2 LOC360821 similar to Putative protein 15E1.2 (LOC360821). 1.98 XM_224170.3 Lrp10 low-density lipoprotein receptor-related protein 10 (Lrp10). 1.98 XM_232283.3 Plxnd1 plexin D1 (Plxnd1). 1.96 XM_340794.2 Rufy1 RUN and FYVE domain containing 1 (Rufy1). 1.94 XM_228615.3 LOC317275 similar to RIKEN cDNA 1500016H10 (LOC317275). 1.88 NM_001004261.1RGD1303232 Phytn_dehydro and Pyr_redox domain containing protein RGD1303232 (RGD1303232). 1.87 NM_080688.1 Plcd4 phospholipase C, delta 4 (Plcd4). 1.86 XM_341896.2 Stim1 stromal interaction molecule 1 (Stim1). 1.85 XM_213833.3 Bloc1s1 biogenesis of lysosome-related organelles complex-1, subunit 1 (Bloc1s1). 1.84 NM_053332.2 Cubn cubilin (intrinsic factor-cobalamin receptor) (Cubn). 1.81 XM_574321.1 LOC499031 similar to kinesin family member 25 isoform 1 (LOC499031). 1.81 XM_341567.2 Plxdc2 plexin domain containing 2 (Plxdc2). 1.80 NM_017026.1 Mbp myelin basic protein (Mbp). 1.79 XM_237395.3 Hes6 hairy and enhancer of split 6 (Drosophila) (Hes6). 1.78 XM_576322.1 LOC500914 similar to basic transcription factor 3 (LOC500914). 1.78 NM_031065.1 Rpl10a ribosomal protein L10A (Rpl10a). 1.78 NM_017351.1 Itih3 inter-alpha trypsin inhibitor, heavy chain 3 (Itih3). 1.74 NM_017138.1 Lamr1 laminin receptor 1 (ribosomal protein SA) (Lamr1). 1.73 NM_031035.2 Gnai2 guanine nucleotide binding protein, alpha inhibiting 2 (Gnai2). 1.73 NM_012695.2 Smp2a senescence marker protein 2A gene, exons 1 and 2 (Smp2a). 1.72 NM_053667.1 Lepre1 leprecan 1 (Lepre1). 1.71 XM_579654.1 Mpst mercaptopyruvate sulfurtransferase (Mpst). 1.70 XM_574198.1 LOC498909 similar to RIKEN cDNA 2310005O14 (LOC498909). 0.59 NM_053714.1 Ank progressive ankylosis homolog (mouse) (Ank). 0.58 XM_576819.1 LOC501407 similar to GTPase activating protein testicular GAP1 (LOC501407). 0.57 XM_580023.1 LOC499837 LOC499837 (LOC499837). 0.57 XM_215752.3 Plekha3 pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3. 0.57 XM_220717.3 Abr active BCR-related gene (Abr). 0.57 XM_219882.3 Cox15 COX15 homolog, cytochrome c oxidase assembly protein (yeast) (Cox15). 0.57 XM_224329.3 LOC306007 similar to 2610301G19Rik protein (LOC306007). 0.56 NM_001007714.1Morf4l2 MORF-related gene X (Morf4l2). 0.56 XM_342911.2 LOC362593 similar to Autoantigen NGP-1 (LOC362593). 0.56 XM_227282.2 Slitrk3 SLIT and NTRK-like family, member 3 (Slitrk3). 0.55 XM_237246.3 LOC501161 similar to Nol5a protein (LOC501161). 0.55 XM_220455.3 LOC303164 similar to hypothetical protein FLJ20531 (LOC303164). 0.55 XM_576334.1 LOC500925 similar to expressed sequence AI836003 (LOC500925). 0.54 NM_001006981.1Dlst dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) (Dlst). 0.54 XM_576206.1 Tra1 tumor rejection antigen gp96 (Tra1). 0.54 XM_214992.3 Alg8 asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase) (Alg8). 0.53 XM_223442.3 LOC305375 similar to Chain A, Human Ubiquitin-Conjugating Enzyme Ubc9 (LOC305375).
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