Development 143: doi:10.1242/dev.127860: Supplementary information gene target species forward reverse Prox1 DNA mouse CTC TGT GGA AAG GAC TCC GAA TC ACA CTA AAC AAG CAA ATG GAA ATG C MLR10Cre DNA mouse CCT GTT TTG CAC GTT CAC CG ATG CTT CTG TCC GTT TGC CG Cdkn1b mRNA mouse GCC AGA CGT AAA CAG CTC CGA ATT A AGG CAG ATG GTT TAA GAG TGC CT Cdkn1C mRNA mouse CAA GCG AAC AGG CAG GCA AGC TCG AAG GCT GGC TGA TTG GTG Maf mRNA mouse GTG GTG GTG ATG GCT CTT TT GTT ACG GGG GAA TTC AGG TT Cryaa mRNA mouse GAG ATT CAC GGC AAA CAC AA ACA TTG GAA GGC AGA CGG TA Cryab mRNA mouse ACT CAA AGT CAA GGT TCT GGG GGG ATG AAG TGA TGG TGA GAG Cryba1 mRNA mouse TGG AGT GTG GCG CCT GGA TT CAT TGC TCC CGC TCC AGG CAT Cryba3/a1 mRNA mouse CCT GGA GCG GGA GCA ATG CC TCA CAG ATT TCC CAC TGG CGT CC Crybb2 mRNA mouse GTG CAG AGC GGC ACG TGG GT TGT CAC GGA TGC GAC GCA CA Crygc mRNA mouse CAT CCC CCA TGC AGG TTC AGC CCG CCT TAG CAT CTA CA Fgfr1 mRNA mouse AGC CCC TCT GGC AGC GAT ACC AGG GAG CTA CAG GCC TAC GGT T Fgfr2 mRNA mouse GGG GGC GCT TCA TCT GCC TG CGG TGC TCC TTC TGG TTC TAA AGT G Fgfr3 mRNA mouse CAG TGT GCG TGT AAC AGA TGC TCC A TCG CTC CGG GCG AGT CCA AT Lctl mRNA mouse GCA CTG GCC TAT ATG TGG CT TAC TAG GCC GTG CTG TTT GC Mafb mRNA mouse GCC TCT TAG ACT TGG GCA GA CCT TCC AGC TTG GAG AA AG Mip mRNA mouse CGT GCT CTG CAT CTT TGC TA ACC CTC CCC ACA GTC TCT TT Pax6 mRNA mouse GCA CAT GCA AAC ACA CAT GA ACT TGG ACG GGA ACT GAC AC Prox1 mRNA mouse AGT AAG ACA TCA CCG CGT GCG C GCT GGG CAC AGC TCA AGA ATC CC Sox1 mRNA mouse GGC CAA GCG GCT GCG CGC GCT GGC CAG CTG CGC CTC CTG CAT Sox2 mRNA mouse GGC AGC TAC AGC ATG ATG CAG GAG C CTG GTC ATG GAG TTG TAC TGC AGG Crybb1 mRNA mouse CAG GGC CTG ATG GCA AGG GAA CCT GCT CGA AGA CGA TCA GCC Cdh1 mRNA mouse GCACTCTTCTCCTGGTCCTG TATGAGGCTGTGGGTTCCCTC Fgfrl1 mRNA mouse TCT TCA GGC TTC AGG TTC TTC AAG C AGG AGG ACC CAG CCA GC 18S rDNA -‐0.15 Kb Crybb1 RNA mouse QUIAGEN PPM57735E-‐200 DNA chicken TCT GTT GTG CCG CTG GAT A CCA GTC ATC ACA TCC TGC AA -‐.05 Kb Spam1 DNA chicken AGC TGC ACT CCA GTC CTT TC GTA GCC TCT GGC ATG GTG TT -‐2 Kb Lctl DNA chicken AGG AAG ATG TCT CAC CCC TGA TCC CTC CTG CAA TAG GTG GTA -‐0.4 Kb Lctl DNA chicken CCC AGT GGG GGA GCA ATA AA TGT ATC GAA GTG ACA TCA GCG -‐0.05 Kb Lctl DNA chicken ATT CAC AGG CTG GAA ACT CC TGT ACA ATG CGG GAG AAG TGA +5 Kb Lctl DNA chicken AGC CTG GCT TGC ATG TGT AT GGA GTG TTC AGA AGT GTG GGA -‐2 Kb Fgfr3 DNA chicken GAG AGG CTC AGA CAC CGA AC AGT CTC CTG CTG AGT GAC CA -‐0.14 Kb Fgfr3 DNA chicken TCC CAT CCC CGT ATT CAG GA ATG TGT TCG GTG TCT GAG CC +5 Kb Fgfr3 DNA chicken ACT GAC TCC ATG CTC TCC CT GCA GGC AGC AAA ACT TCC AA -‐2 Kb Fgfrl1 -‐0.038 Kb Fgfrl1 DNA chicken TCT GGA TGC CCA AAG ATG GAG TGC CTC CTG TAG ACT TTC CCA DNA chicken AGC TCA TCT CAG GAA ACG GC CAT AGG CTG CGT GTC CAT CT -‐0.15 Kb Fgfrl1 DNA chicken TGC CCG TGG CGG TTG AGC TCC AAA CTT CGC TCC AA +5 Kb Fgfrl1 DNA chicken TTC TCT CTG CAC CAC TTG GC TAG TCC CAA CAA CAC GTT CCC Prox1 mRNA chicken AGA TGG AGA AGT ATG CGC GG CTG GAA CCT CAA AGT CAT TCG C Fgfr1 mRNA chicken GGG GTA CAA GGT CCG CTA TG GTG TGG TTG ATG CTC CCG TA Fgfr2 mRNA chicken TCT GCC AGC TCC TGA AAA GG TTC TTC ATG CGG CAC AGG AT Fgfr3 mRNA chicken GGA AAC CCA ACT CCC ACC AT GCT GGT GTC GCA ACT TGA TG Fgfrl1 mRNA chicken CAG TCC TGC CAG ATC CCA AG GCA AAG CCA CAG GAG GAT TG Lctl mRNA chicken TCA CAC TCT GCA TAC TCA CCA G ACA GCT GGC TTA CTG TAT TGT 18s mRNA chicken TGT GCC GCT AGA GGT GAA ATT TGG CAA ATG CTT TCG CTT T Development • Supplementary information Supplementary Table 1: primers Development 143: doi:10.1242/dev.127860: Supplementary information Gene Symbol Antibody Sample Prep Fixation Blocking Primary secondary final wash Prox1 from Duncan MK et al. 2002 Frozen tissue was sectioned (16uM) and stored at -‐80C immersion in 1:1 acetone/methanol at -‐ 20C for 15 minutes, then slides were air dried Slides were immersed in 1% Bovine Serum Albumin (BSA) in Phosphate buffered saline (PBS) for 1 hour at room temperature (RT). Primary antibody was diluted 1:500 in blocking buffer, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were then washed 3 times for 5 minutes in PBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with PBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. cMaf Santa Cruz: sc-‐ 7866 Frozen tissue was sectioned (16uM) and stored at -‐80C immersion in 1:1 acetone/methanol at -‐ 20C for 15 minutes, then slides were air dried Slides were immersed in 1% Bovine Serum Albumin (BSA) in Phosphate buffered saline (PBS) for 1 hour at room temperature (RT). Primary antibody was diluted 1:100 in blocking buffer, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were then washed 3 times for 5 minutes in PBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with PBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. Pax6 Santa Cruz: sc-‐ 53106 Frozen tissue was sectioned (16uM) and stored at -‐80C immersion in 4% paraformaldehyde (pfa) in PBS for 20 min @ RT, then slides were washed in tris buffered saline (TBS) for 5 minutes. Samples were covered with 5% normal goat serum in TBS supplemented with .3% Triton x100 Primary antibody was diluted 1:200 in blocking buffer, and applied to tissue overnight in a humid slide chamber at 4C. Slides were then washed 3 times for 10 minutes in TBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with TBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. ECad Cell Signaling : 4065 Frozen tissue was sectioned (16uM) and stored at -‐80C immersion in 4% paraformaldehyde (pfa) in PBS for 20 min @ RT, then slides were washed in tris buffered saline (TBS) for 5 minutes. Samples were covered with 5% normal goat serum in TBS supplemented with .3% Triton x100 Primary antibody was diluted 1:100 in blocking buffer, and applied to tissue overnight in a humid slide chamber at 4C. Slides were then washed 3 times for 10 minutes in TBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with TBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. Cdnk1b Kip1 (p27 ) Santa Cruz: sc-‐ 528 Frozen tissue was sectioned (16uM) and stored at -‐80C immersion in 4% paraformaldehyde (pfa) in PBS for 20 min @ RT, then slides were washed in tris buffered saline (TBS) for 5 minutes. Samples were covered with 5% normal goat serum in TBS supplemented with .3% Triton x100 Primary antibody was diluted 1:100 in blocking buffer, and applied to tissue overnight in a humid slide chamber at 4C. Slides were then washed 3 times for 10 minutes in TBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with TBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. Mip (Aqp0) Millipore : AB3071 Frozen tissue was sectioned (16uM) and stored at -‐80C immersion in 1:1 acetone/methanol at -‐ 20C for 15 minutes, then slides were air dried Slides were immersed in 1% Bovine Serum Albumin (BSA) in Phosphate buffered saline (PBS) for 1 hour at room temperature (RT). Primary antibody was diluted 1:100 in blocking buffer, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were then washed 3 times for 5 minutes in PBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 1 hour at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with PBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. Development • Supplementary information Supplementary Table 2: immunofluorescence and immunohistochemistry procedures Cdkn 1c (p57 Kip2 ) Santa Cruz: sc-‐ 8298 Paraffin embedded tissue was sectioned (6uM) and stored at RT sections were dewaxed by two five minute immersions in xylenes, then 2 minute immersions in decreasing concentrations of ethanol in water (100%, 95%, 70%, 50%) followed by a brief rinse in running distilled water. Antigen retrieval: slides were double boiled in 0.1M Sodium citrate pH6.0 for 30 minutes, and allowed to cool for 10 minutes. Slides were rinsed in dH2O for 2 minutes and washed in PBS for 5 minutes. Slides were immersed in 1% Saponin in PBS for 5 minutes, followed by 3 5 minute immersions in PBS with 0.1% Tween 20 (PBS-‐T). Slides were then blocked in 10% NGS in PBST for 30 minutes at RT. Primary antibody was diluted 1:100 in blocking buffer, and applied to tissue overnight in a humid slide chamber at 4C. Slides were then washed 3 times for 10 minutes in PBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 2 hours at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with PBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. Cryg (gamma-‐ crystallin ) Santa Cruz: sc-‐ 22415 Frozen tissue was sectioned (16uM) and stored at -‐80C immersion in 4% paraformaldehyde (pfa) in PBS for 20 min @ RT, then slides were washed in tris buffered saline (PBS) for 5 minutes. Samples were covered with 5% normal chicken serum in PBS supplimented with .3% Triton x100 Primary antibody was diluted 1:100 in blocking buffer, and applied to tissue for 4 hours in a humid slide chamber at RT. Slides were then washed 3 times for 10 minutes in PBS. Secondary Alexafluor 568 conjugated anti-‐rabbit antibody was diluted 1:200 in blocking buffer with 1:2000 Draq5, and applied to tissue for 2 hours at RT in a humid slide chamber. Slides were washed 3 times for ten minutes with PBS then covered with mounting media, coverslipped and sealed, slides were stored at -‐20C until imaged. Cryb (beta-‐ crystallin gift from Samuel Zigler, Johns Hopkins Universit y , MD) Paraffin embedded tissue was sectioned (6uM) and stored at RT Samples were processed using the Dako Envision horseraddish peroxidase (HRP) kit. Endogenous peroxides were eliminated covering samples with peroxidase blocking solution. Primary antibody was diluted 1:600 in PBST and incubated in a humid slide chamber for 30 minutes at RT. Slides were treated with anti rabbit conjugated HRP for 30 min and washed in PBS 3 times for five minutes. Slides were treated with 3,3'-‐diaminobenzidine (DAB) chromogen in pairs of controls and experimental slides until the tissue was visibly stained. Slides were counterstained with Hematoxylin, and dehydrated and sealed according to our H&E protocol. p-‐ERK (phosph orylated ERK Cell Signaling : 4377s Paraffin embedded tissue was sectioned (6uM) and stored at RT paraffin sections were de-‐waxed by two immersions in Citrus Clearing Solvent for 10 minutes. Samples were rehydrated by immersion in decreeing concentrations of ethanol in water (100% 3x 3min, 95% 3x 2min, 70% 2 min. paraffin sections were de-‐waxed by two immersions in Citrus Clearing Solvent for 10 minutes. Samples were rehydrated by immersion in decreeing concentrations of ethanol in water (100% 3x 3min, 95% 3x 2min, 70% 2 min. Antigen retrieval: slides were double boiled in 0.1M Sodium citrate pH6.0 for 30 minutes, and allowed to cool for 10 minutes. Slides were rinsed in dH2O for 2 minutes and washed in PBS for 5 minutes. Slides were immersed in 1% Saponin in PBS for 5 minutes, followed by 3 5 minute immersions in PBS with 0.1% Tween 20 (PBS-‐T). Slides were then blocked in 10% NGS in PBST for 30 minutes at RT. Slides were processed using the standard procedure outlined in the CSAII Biotin-‐Free Tyramide Signal Amplification kit with the CSAII rabbit link addition from DAKO. Primary antibody was diluted 1:50. Slides were counterstained with Hematoxylin, and dehydrated and sealed according to our H&E protocol. Development • Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information Cell Signaling : 9271s Paraffin embedded tissue was sectioned (6uM) and stored at RT paraffin sections were de-‐waxed by two immersions in Citrus Clearing Solvent for 10 minutes. Sampes were rehydrated by immersion in decreseing concentrations of ethanol in water (100% 3x 3min, 95% 3x 2min, 70% 2 min. Antigen retreival: slides were double boiled in 0.1M Sodium citrate pH6.0 for 30 minutes, and allowed to cool for 10 minutes. Slides were rinsed in dH2O for 2 minutesand washed in PBS for 5 minutes. Slides were immersed in 1% Saponin in PBS for 5 minutes, followed by 3 5 minute immersions in PBS with 0.1% Tween 20 (PBS-‐T). Slides were then blocked in 10% NGS in PBST for 30 minutes at RT. Slides were processed using the standard procedure outlined in the CSAII Biotin-‐Free Tyramide Signal Amplification kit with the CSAII rabbit link addition from DAKO. Primary antibody was diluted 1:50. Slides were counterstained with Hematoxylin, and dehydrated and sealed according to our H&E protocol. Development • Supplementary information p-‐AKT (Phosph orylated AKT) Development 143: doi:10.1242/dev.127860: Supplementary information feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean Lctl Dnase2b Birc7 D630024D03Rik Tmprss11e Crygf Bfsp1 Crygb Scn11a Drd4 Hopx Scnn1b Gm20757 Crygd Hspb3 Sct Gm14546 Pgam2 Plekhs1 Myo18b Slc24a4 Gcg Myo7b Wnt7a Bcmo1 1700080G11Rik Crygs Gm26847 Cryga St18 Snx22 Cryba2 S100a4 Chrng Cryba4 Syn2 Crygc 1500009C09Rik Prox1os Sec14l5 Cryge Rspo1 Mip Bmper Pla2g7 Ermap Lyzl4 Gje1 Hsf4 Crybb1 -‐190.8 -‐73.3 -‐68.0 -‐64.5 -‐61.6 -‐52.6 -‐39.2 -‐38.7 -‐31.0 -‐30.4 -‐25.5 -‐23.2 -‐23.1 -‐21.6 -‐21.3 -‐21.2 -‐20.5 -‐20.3 -‐20.0 -‐19.6 -‐19.2 -‐18.7 -‐18.2 -‐17.5 -‐16.7 -‐16.5 -‐16.0 -‐15.9 -‐15.8 -‐15.7 -‐15.6 -‐15.6 -‐15.4 -‐15.3 -‐14.8 -‐14.8 -‐14.6 -‐13.7 -‐13.6 -‐13.6 -‐13.5 -‐13.5 -‐13.4 -‐12.9 -‐12.6 -‐12.4 -‐12.3 -‐12.0 -‐11.7 -‐11.6 1.7E-‐13 4.4E-‐11 2.9E-‐14 1.4E-‐10 1.4E-‐06 3.6E-‐15 2.9E-‐22 1.7E-‐21 8.9E-‐52 6.5E-‐76 2.3E-‐22 2.2E-‐47 2.9E-‐14 1.3E-‐31 5.9E-‐35 3.9E-‐16 3.1E-‐19 9.8E-‐33 6.7E-‐24 1.4E-‐22 1E-‐28 4.6E-‐44 1.9E-‐18 1.3E-‐24 1.9E-‐25 7.7E-‐10 8E-‐35 8.1E-‐46 5.2E-‐31 3.8E-‐38 1E-‐16 4.9E-‐46 6.7E-‐14 1.9E-‐41 5.8E-‐37 1.9E-‐57 4.6E-‐35 3.7E-‐33 1.1E-‐48 7.6E-‐37 5.1E-‐38 7.1E-‐79 7.5E-‐45 7E-‐40 2.9E-‐24 1.1E-‐24 3.1E-‐39 2.6E-‐45 1.6E-‐41 8E-‐49 ENSMUSG00000032401 ENSMUSG00000028185 ENSMUSG00000038840 ENSMUSG00000085772 ENSMUSG00000054537 ENSMUSG00000025945 ENSMUSG00000027420 ENSMUSG00000073658 ENSMUSG00000034115 ENSMUSG00000025496 ENSMUSG00000059325 ENSMUSG00000030873 ENSMUSG00000098040 ENSMUSG00000067299 ENSMUSG00000051456 ENSMUSG00000038580 ENSMUSG00000086762 ENSMUSG00000020475 ENSMUSG00000035818 ENSMUSG00000072720 ENSMUSG00000041771 ENSMUSG00000000394 ENSMUSG00000024388 ENSMUSG00000030093 ENSMUSG00000031845 ENSMUSG00000086771 ENSMUSG00000033501 ENSMUSG00000097526 ENSMUSG00000044429 ENSMUSG00000033740 ENSMUSG00000039452 ENSMUSG00000006546 ENSMUSG00000001020 ENSMUSG00000026253 ENSMUSG00000066975 ENSMUSG00000009394 ENSMUSG00000025952 ENSMUSG00000068099 ENSMUSG00000079045 ENSMUSG00000091712 ENSMUSG00000070870 ENSMUSG00000028871 ENSMUSG00000025389 ENSMUSG00000031963 ENSMUSG00000023913 ENSMUSG00000028644 ENSMUSG00000032530 ENSMUSG00000019867 ENSMUSG00000033249 ENSMUSG00000029343 0.03 0.12 0.14 0.08 0.09 92.23 18.66 276.61 0.15 0.61 0.92 1.53 1.95 318.25 1.24 0.20 0.17 11.10 0.44 0.29 1.46 1.45 0.49 1.31 0.27 0.15 18.08 12.78 1003.75 0.20 1.12 382.22 1.68 5.24 896.00 0.82 340.35 0.61 6.81 0.54 1025.95 4.59 159.97 4.19 16.92 0.71 1.21 3.93 7.13 2318.10 2.91 5.55 6.78 3.60 4.03 3723.47 555.71 8240.52 3.53 12.18 17.11 26.32 33.54 5283.50 17.73 3.35 2.44 171.23 6.50 4.23 21.32 19.19 6.71 17.08 3.35 2.53 220.23 156.15 12221.23 2.22 13.06 4600.10 17.59 61.97 10270.19 8.99 3804.70 5.75 70.17 4.97 10704.19 47.02 1657.29 41.69 162.56 6.54 10.96 35.61 63.67 20757.30 Ndrg1 Mafa Gpr160 Cryba1 Ggct 1300017J02Rik Tmem179 Bfsp2 Lim2_2 Caprin2 Tmem40 Cabp5 Tmod1 Fam89a B230206L02Rik Dmtn Zfp365 Crybb3 Pgm5 Scgn Cela1 Fgfr3 Hfe Gsn Nol3 Dync1i1 Grifin Mtnr1a Myh7b Gm15417 Capn3 Gstp2 Gadd45b Tdrd7 Trpc6 Poln Lgi2 Spta1 Nrcam Crygn Slc46a3 Akap14 Pip5kl1 Unc13c Epn3 Osbp2 Tmem252 Gls2 Cend1 Stx11 -‐11.4 -‐11.3 -‐11.1 -‐11.1 -‐10.9 -‐10.7 -‐10.5 -‐10.4 -‐10.4 -‐10.3 -‐10.3 -‐10.2 -‐10.2 -‐10.1 -‐10.0 -‐9.8 -‐9.8 -‐9.6 -‐9.6 -‐9.5 -‐9.3 -‐9.3 -‐9.3 -‐9.2 -‐8.9 -‐8.7 -‐8.5 -‐8.4 -‐8.4 -‐8.2 -‐8.0 -‐7.9 -‐7.9 -‐7.8 -‐7.8 -‐7.6 -‐7.5 -‐7.5 -‐7.4 -‐7.4 -‐7.3 -‐7.1 -‐7.0 -‐7.0 -‐6.9 -‐6.8 -‐6.8 -‐6.7 -‐6.7 -‐6.4 1.4E-‐16 2.7E-‐33 2.6E-‐83 3.9E-‐42 2E-‐26 1.4E-‐65 1.6E-‐09 4E-‐26 9.4E-‐41 7.8E-‐37 6.3E-‐47 1.1E-‐10 1.8E-‐56 1.5E-‐33 1.4E-‐08 7.7E-‐54 9E-‐51 4.8E-‐42 2E-‐33 1.1E-‐23 1.3E-‐61 3.8E-‐55 8.6E-‐25 3.9E-‐45 1.2E-‐38 1.4E-‐20 3.8E-‐51 8.9E-‐32 8.2E-‐32 7.2E-‐09 9.8E-‐56 1E-‐12 6.5E-‐12 4.5E-‐42 2.4E-‐26 7.5E-‐13 7.6E-‐37 1.4E-‐38 2E-‐38 1.6E-‐44 3.3E-‐19 5.1E-‐22 8E-‐86 6.6E-‐19 2.8E-‐39 3.6E-‐54 1E-‐19 4.1E-‐22 9.8E-‐25 1.7E-‐05 ENSMUSG00000005125 ENSMUSG00000047591 ENSMUSG00000037661 ENSMUSG00000000724 ENSMUSG00000002797 ENSMUSG00000033688 ENSMUSG00000054013 ENSMUSG00000032556 NA ENSMUSG00000030309 ENSMUSG00000059900 ENSMUSG00000005649 ENSMUSG00000028328 ENSMUSG00000043068 ENSMUSG00000086003 ENSMUSG00000022099 ENSMUSG00000037855 ENSMUSG00000029352 ENSMUSG00000041731 ENSMUSG00000021337 ENSMUSG00000023031 ENSMUSG00000054252 ENSMUSG00000006611 ENSMUSG00000026879 ENSMUSG00000014776 ENSMUSG00000029757 ENSMUSG00000036586 ENSMUSG00000054764 ENSMUSG00000074652 ENSMUSG00000074466 ENSMUSG00000079110 ENSMUSG00000038155 ENSMUSG00000015312 ENSMUSG00000035517 ENSMUSG00000031997 ENSMUSG00000045102 ENSMUSG00000039252 ENSMUSG00000026532 ENSMUSG00000020598 ENSMUSG00000038135 ENSMUSG00000029650 ENSMUSG00000036551 ENSMUSG00000046854 ENSMUSG00000062151 ENSMUSG00000010080 ENSMUSG00000020435 ENSMUSG00000048572 ENSMUSG00000044005 ENSMUSG00000060240 ENSMUSG00000039232 0.67 1.24 1.55 976.24 1.46 1.62 0.33 19.66 31.34 20.60 15.31 0.34 1.79 4.59 0.27 1.75 8.10 1301.62 3.00 0.69 10.47 5.26 2.12 29.53 1.39 0.94 40.47 1.91 1.23 1.21 224.71 1.43 1.29 59.33 3.36 0.39 6.68 0.50 9.31 535.02 1.52 0.93 5.34 0.62 0.72 6.72 1.46 0.43 1.18 0.76 5.68 10.27 12.93 8287.86 12.15 13.03 2.53 155.26 249.57 163.11 120.59 2.56 13.66 34.86 2.09 12.88 61.18 9556.74 21.79 5.22 74.85 37.60 14.78 210.46 9.21 6.07 263.22 12.17 7.86 7.50 1401.46 8.34 7.46 354.57 19.73 2.16 38.45 2.88 53.58 3026.93 8.31 4.99 29.05 3.23 3.83 35.42 7.40 2.25 5.77 3.66 Development • Supplementary information Supplementary Table 3: genes down-‐regulated following Prox1 loss feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean Zbtb7b Pla2g16 Gm11427 Rsph10b Lingo3 RP23-‐380A10.3 Cryaa Prkca Pygm Thsd4 R3hdml Akr1b8 Cpeb3 Zmat4 Kcnma1 Lin7a Rcan2 Pon2 Cd24a Stat5a Gm14005 Nyap1 Fam131a Add2 Arntl2 Espn Arhgdig Ptgfr Htatip2 Efcab10 2900005J15Rik B230312C02Rik Gm17586 Gja3 Lsamp Gss Zfp185 Nkg7 Mboat1 Rnaset2b Paqr7 Synm Gstp1 Clgn Sqrdl Sorbs1 Aldoc Hebp2 Wnt7b Metrnl -‐6.5 -‐6.4 -‐6.3 -‐6.3 -‐6.2 -‐6.2 -‐6.2 -‐6.2 -‐6.1 -‐6.1 -‐6.0 -‐6.0 -‐5.9 -‐5.9 -‐5.8 -‐5.8 -‐5.8 -‐5.8 -‐5.7 -‐5.7 -‐5.6 -‐5.5 -‐5.5 -‐5.4 -‐5.4 -‐5.3 -‐5.3 -‐5.3 -‐5.3 -‐5.2 -‐5.2 -‐5.2 -‐5.2 -‐5.2 -‐5.1 -‐5.1 -‐5.1 -‐5.1 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐5.0 -‐4.9 4.9E-‐11 1.7E-‐23 3.7E-‐11 1.4E-‐12 3.6E-‐32 3.4E-‐06 4E-‐42 1.8E-‐35 2.7E-‐48 1.3E-‐11 2.7E-‐18 9.3E-‐22 6.8E-‐14 1.3E-‐18 4.8E-‐31 1.2E-‐50 2E-‐36 1.1E-‐38 1.2E-‐40 4.7E-‐28 4.4E-‐09 3.6E-‐57 3.1E-‐36 1.1E-‐33 7.5E-‐29 8.9E-‐44 5.3E-‐23 8.1E-‐17 6.7E-‐10 3.3E-‐06 1.1E-‐11 4.4E-‐42 2E-‐32 5.5E-‐38 3.7E-‐22 3.4E-‐30 1.1E-‐49 2.7E-‐08 4.9E-‐41 1.3E-‐23 6.9E-‐31 9.5E-‐23 5.5E-‐30 9.2E-‐31 1.9E-‐27 2.1E-‐20 3.6E-‐28 1.9E-‐44 4.7E-‐22 1E-‐35 ENSMUSG00000028042 ENSMUSG00000060675 ENSMUSG00000083161 ENSMUSG00000075569 ENSMUSG00000051067 NA ENSMUSG00000024041 ENSMUSG00000050965 ENSMUSG00000032648 ENSMUSG00000032289 ENSMUSG00000078949 ENSMUSG00000029762 ENSMUSG00000039652 ENSMUSG00000037492 ENSMUSG00000063142 ENSMUSG00000019906 ENSMUSG00000039601 ENSMUSG00000032667 ENSMUSG00000047139 ENSMUSG00000004043 ENSMUSG00000074813 ENSMUSG00000045348 ENSMUSG00000050821 ENSMUSG00000030000 ENSMUSG00000040187 ENSMUSG00000028943 ENSMUSG00000073433 ENSMUSG00000028036 ENSMUSG00000039745 ENSMUSG00000020562 ENSMUSG00000043833 ENSMUSG00000084843 ENSMUSG00000097062 ENSMUSG00000048582 ENSMUSG00000061080 ENSMUSG00000027610 ENSMUSG00000031351 ENSMUSG00000004612 ENSMUSG00000038732 ENSMUSG00000094724 ENSMUSG00000037348 ENSMUSG00000030554 ENSMUSG00000060803 ENSMUSG00000002190 ENSMUSG00000005803 ENSMUSG00000025006 ENSMUSG00000017390 ENSMUSG00000019853 ENSMUSG00000022382 ENSMUSG00000039208 2.03 12.55 0.54 0.67 0.92 0.45 15055.37 1.77 22.49 1.24 6.20 1.10 0.46 0.71 0.89 4.10 2.01 14.97 342.95 0.85 0.62 11.28 3.43 5.99 1.39 1.52 0.88 2.54 0.74 0.58 0.78 7.32 18.44 69.21 1.08 6.90 12.06 0.52 11.52 1.80 2.00 10.57 52.86 1.24 1.21 4.65 2.27 5.02 13.42 7.34 9.93 61.54 2.74 3.17 4.47 2.00 71641.20 8.31 106.00 5.76 28.28 5.39 2.02 3.15 3.86 18.34 8.75 66.29 1517.01 3.65 2.63 48.42 14.48 24.93 5.68 6.18 3.59 10.28 2.71 2.58 3.21 29.36 73.00 274.68 4.28 27.08 47.51 2.11 44.52 6.87 7.67 40.79 202.87 4.76 4.57 17.79 8.52 19.03 50.96 27.71 Fn3krp Rab42 Ogn Rnf180 Prkaa2 Hist1h2bc Cyb5r2 Rnf19b Fam46c Ace Qpct Entpd1 Vit Ndrg4 Tnfrsf23 Gm11961 Pstpip2 Rgs8 Cnih2 Gpr19 Itpk1 Itga2 Gprc5b Fgfrl1 Dner Sptb Map6d1 Dbnl Jazf1 S1pr5 Btbd17 Hist2h3c2 Magi2_1 Tex2 Snhg12 Adc Tob1 Cdkl2 Abtb2 Reep1 Adra2a Metap1 Optn Tecrl Stk39 Fam46b Kif1a Pmp22 Cyyr1 Clu -‐4.9 -‐4.9 -‐4.9 -‐4.8 -‐4.7 -‐4.7 -‐4.7 -‐4.7 -‐4.6 -‐4.6 -‐4.5 -‐4.5 -‐4.5 -‐4.5 -‐4.5 -‐4.5 -‐4.5 -‐4.5 -‐4.4 -‐4.4 -‐4.4 -‐4.4 -‐4.4 -‐4.4 -‐4.4 -‐4.4 -‐4.3 -‐4.3 -‐4.3 -‐4.3 -‐4.3 -‐4.2 -‐4.2 -‐4.2 -‐4.2 -‐4.2 -‐4.1 -‐4.1 -‐4.1 -‐4.0 -‐4.0 -‐4.0 -‐4.0 -‐4.0 -‐4.0 -‐4.0 -‐4.0 -‐4.0 -‐4.0 -‐3.9 9E-‐33 2.9E-‐09 8.4E-‐13 6.4E-‐06 3.6E-‐25 3.8E-‐35 7.1E-‐12 6.8E-‐30 1.1E-‐29 2.5E-‐22 1.6E-‐22 4.5E-‐32 9.6E-‐43 5.3E-‐48 8.6E-‐20 4.8E-‐12 6E-‐08 3E-‐51 9.7E-‐40 1.2E-‐37 4E-‐34 1.6E-‐13 2.4E-‐35 2.1E-‐28 4.4E-‐11 1E-‐19 1E-‐27 1E-‐36 1E-‐52 1.5E-‐17 7.7E-‐40 1.1E-‐09 1.1E-‐07 8.8E-‐26 1.6E-‐17 1.1E-‐20 3.2E-‐24 2.8E-‐20 3E-‐19 4.6E-‐37 4.9E-‐19 2.3E-‐29 1.4E-‐10 3.5E-‐07 1.3E-‐36 0.00012 1.3E-‐13 1.1E-‐27 1.2E-‐16 1.9E-‐23 ENSMUSG00000039253 ENSMUSG00000089687 ENSMUSG00000021390 ENSMUSG00000021720 ENSMUSG00000028518 ENSMUSG00000018102 ENSMUSG00000048065 ENSMUSG00000028793 ENSMUSG00000044468 ENSMUSG00000020681 ENSMUSG00000024084 ENSMUSG00000048120 ENSMUSG00000024076 ENSMUSG00000036564 ENSMUSG00000037613 ENSMUSG00000056288 ENSMUSG00000025429 ENSMUSG00000042671 ENSMUSG00000024873 ENSMUSG00000032641 ENSMUSG00000057963 ENSMUSG00000015533 ENSMUSG00000008734 ENSMUSG00000008090 ENSMUSG00000036766 ENSMUSG00000021061 ENSMUSG00000041205 ENSMUSG00000020476 ENSMUSG00000063568 ENSMUSG00000045087 ENSMUSG00000000202 ENSMUSG00000081058 NA ENSMUSG00000040548 ENSMUSG00000086290 ENSMUSG00000028789 ENSMUSG00000037573 ENSMUSG00000029403 ENSMUSG00000032724 ENSMUSG00000052852 ENSMUSG00000033717 ENSMUSG00000005813 ENSMUSG00000026672 ENSMUSG00000049537 ENSMUSG00000027030 ENSMUSG00000046694 ENSMUSG00000014602 ENSMUSG00000018217 ENSMUSG00000041134 ENSMUSG00000022037 13.59 0.88 2.81 2.50 2.52 16.19 0.65 10.89 25.12 0.74 3.99 3.85 77.18 4.42 1.28 1.53 1.27 6.33 10.49 5.07 5.66 1.69 19.39 14.83 1.56 19.31 2.53 59.24 6.48 1.32 5.19 1.12 0.77 5.42 21.58 3.64 39.37 0.98 3.73 12.02 0.91 33.44 4.45 0.85 19.00 0.84 14.51 24.44 4.04 30.72 51.36 3.87 10.42 8.98 9.12 58.74 2.31 38.89 90.13 2.58 13.99 13.38 270.98 15.31 4.32 5.39 4.16 21.93 36.04 17.33 19.17 5.69 65.84 50.00 5.17 65.48 8.41 198.23 21.77 4.35 17.26 3.51 2.46 17.49 68.97 11.57 125.10 3.07 11.59 37.56 2.78 103.99 13.59 2.66 59.09 2.54 44.61 74.78 12.34 93.71 Development • Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean Ctnna2 Id2 Gck Vwa5a Gpr137b-‐ps Mturn Casp7 Tppp3 Rnf113a1 Dock5 Ndufs5 Il18 Fibin Mocs2 Tsc2 Syt5 Prkag2 Rfx8 Sptbn1 Rilpl1 Kcnj11 Serpinb6b Tubb2a Efcab1 Abcc8 Gpm6b Cpne7 Nap1l4 Gadd45g Cpeb2 Map6 Osbpl11 Ptplad2 Cpeb1 Bpnt1 Dgkg Ell2 Atp8a1 Pde2a Fxyd1 Dnmbp Nexn Ngef Herc4 Rnf123 Lyrm1 Pdlim1 Rab3b Rnaset2a Nacc2 -‐3.9 -‐3.9 -‐3.9 -‐3.9 -‐3.9 -‐3.9 -‐3.9 -‐3.9 -‐3.8 -‐3.8 -‐3.8 -‐3.8 -‐3.7 -‐3.7 -‐3.7 -‐3.7 -‐3.7 -‐3.7 -‐3.7 -‐3.7 -‐3.6 -‐3.6 -‐3.6 -‐3.6 -‐3.6 -‐3.6 -‐3.6 -‐3.6 -‐3.5 -‐3.5 -‐3.5 -‐3.5 -‐3.5 -‐3.4 -‐3.4 -‐3.4 -‐3.4 -‐3.4 -‐3.3 -‐3.3 -‐3.3 -‐3.3 -‐3.3 -‐3.2 -‐3.2 -‐3.2 -‐3.2 -‐3.2 -‐3.2 -‐3.2 4E-‐42 3.7E-‐45 2.5E-‐36 3E-‐24 5.9E-‐11 4.4E-‐25 8.4E-‐19 7.4E-‐39 4.8E-‐09 5E-‐19 9.2E-‐13 5.7E-‐08 0.0001 1E-‐23 2.5E-‐15 7E-‐12 1.8E-‐32 5.8E-‐09 1.4E-‐19 1E-‐35 9.5E-‐12 1.8E-‐08 3.7E-‐31 1.5E-‐35 1.7E-‐28 3.6E-‐14 6.8E-‐16 2E-‐31 6E-‐13 4.3E-‐23 3.7E-‐43 7.5E-‐29 1.2E-‐24 4.5E-‐34 2.3E-‐43 1.8E-‐10 1.7E-‐26 1.6E-‐14 6.3E-‐11 2.6E-‐08 7.8E-‐20 1.2E-‐18 4.5E-‐30 2.7E-‐28 8.6E-‐27 2.2E-‐12 1.7E-‐13 1.8E-‐19 9.7E-‐09 2E-‐16 ENSMUSG00000063063 ENSMUSG00000020644 ENSMUSG00000041798 ENSMUSG00000023186 ENSMUSG00000097715 ENSMUSG00000038065 ENSMUSG00000025076 ENSMUSG00000014846 ENSMUSG00000036537 ENSMUSG00000044447 ENSMUSG00000028648 ENSMUSG00000039217 ENSMUSG00000074971 ENSMUSG00000015536 ENSMUSG00000002496 ENSMUSG00000004961 ENSMUSG00000028944 ENSMUSG00000057173 ENSMUSG00000020315 ENSMUSG00000029392 ENSMUSG00000096146 ENSMUSG00000042842 ENSMUSG00000058672 ENSMUSG00000068617 ENSMUSG00000040136 ENSMUSG00000031342 ENSMUSG00000034796 ENSMUSG00000059119 ENSMUSG00000021453 ENSMUSG00000039782 ENSMUSG00000055407 ENSMUSG00000022807 ENSMUSG00000028497 ENSMUSG00000025586 ENSMUSG00000026617 ENSMUSG00000022861 ENSMUSG00000001542 ENSMUSG00000037685 ENSMUSG00000030653 ENSMUSG00000036570 ENSMUSG00000025195 ENSMUSG00000039103 ENSMUSG00000026259 ENSMUSG00000020064 ENSMUSG00000041528 ENSMUSG00000030922 ENSMUSG00000055044 ENSMUSG00000003411 ENSMUSG00000095687 ENSMUSG00000026932 2.34 60.12 5.95 9.90 1.28 7.59 14.37 7.65 25.74 9.10 4.74 1.47 2.05 8.37 22.41 1.82 6.96 0.83 32.36 28.59 2.65 0.95 17.02 12.03 3.22 4.88 0.97 236.18 9.36 5.21 6.19 14.83 4.69 6.15 14.22 0.80 52.22 1.48 8.34 2.85 9.66 3.19 4.55 32.19 6.21 2.48 3.32 2.55 1.61 2.08 7.13 183.57 18.14 29.97 3.72 22.69 42.48 22.95 74.72 27.10 13.92 4.41 5.80 23.91 63.47 5.08 19.74 2.26 92.67 81.06 7.43 2.59 47.80 33.77 9.07 13.42 2.71 653.88 25.26 14.14 16.82 39.87 12.53 16.32 37.85 2.06 137.46 3.87 21.23 7.36 24.52 8.08 11.50 80.77 15.53 6.24 8.13 6.33 4.06 5.07 Arvcf Kcnq4 Adamts18 Tmem9b Rpl34 Blvra B3gnt5 Tbc1d22a Gm11837 Adamtsl4 Cars Slain1 Gpr137b Nudt22 Rexo2 Gm14295 Fgfbp3 Rasl11b Kif26b Ddx26b Lnp Cttnbp2 Hlcs Pnpla6 Cbs Sntb1 Pbx4 Adam9 Gas6 Ppip5k2 Zfp385a Insig1 Igsf9 Nabp1 Peli1 E530001K10Rik Gls Gm13152 Gm5607 Aldh1a7 Snap91 Sardh C2cd2l Scamp5 Megf9 Dnajb2 Hmgn3 Mecr Sowaha Mob3b -‐3.2 -‐3.2 -‐3.2 -‐3.2 -‐3.2 -‐3.1 -‐3.1 -‐3.1 -‐3.1 -‐3.1 -‐3.1 -‐3.1 -‐3.1 -‐3.1 -‐3.0 -‐3.0 -‐3.0 -‐3.0 -‐3.0 -‐3.0 -‐3.0 -‐3.0 -‐3.0 -‐2.9 -‐2.9 -‐2.9 -‐2.9 -‐2.9 -‐2.9 -‐2.9 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 -‐2.8 4E-‐24 1.3E-‐25 5.5E-‐29 4.1E-‐25 6.2E-‐06 3.3E-‐14 5.6E-‐22 1.6E-‐18 1.3E-‐10 8.2E-‐09 4.7E-‐20 2.5E-‐31 2.1E-‐22 1.4E-‐15 2.8E-‐21 1E-‐10 7.7E-‐14 1.5E-‐25 0.00017 1.2E-‐20 2.1E-‐19 1.2E-‐19 1.7E-‐25 1.3E-‐39 2.5E-‐11 3E-‐11 2.4E-‐14 1.1E-‐25 1.6E-‐16 8.1E-‐28 6E-‐32 2.8E-‐28 2.4E-‐21 2.9E-‐14 4.1E-‐24 6.2E-‐08 2.6E-‐21 6.3E-‐09 4.7E-‐19 7.2E-‐20 1.6E-‐19 6.8E-‐07 5.8E-‐29 1.6E-‐11 6E-‐14 3.6E-‐18 6.4E-‐11 2.9E-‐22 7.6E-‐22 1.2E-‐16 ENSMUSG00000000325 ENSMUSG00000028631 ENSMUSG00000053399 ENSMUSG00000031021 ENSMUSG00000062006 ENSMUSG00000001999 ENSMUSG00000022686 ENSMUSG00000051864 ENSMUSG00000086587 ENSMUSG00000015850 ENSMUSG00000010755 ENSMUSG00000055717 ENSMUSG00000021306 ENSMUSG00000037349 ENSMUSG00000032026 ENSMUSG00000078877 ENSMUSG00000047632 ENSMUSG00000049907 ENSMUSG00000026494 ENSMUSG00000035967 ENSMUSG00000009207 ENSMUSG00000000416 ENSMUSG00000040820 ENSMUSG00000004565 ENSMUSG00000024039 ENSMUSG00000060429 ENSMUSG00000031860 ENSMUSG00000031555 ENSMUSG00000031451 ENSMUSG00000040648 ENSMUSG00000000552 ENSMUSG00000045294 ENSMUSG00000037995 ENSMUSG00000026107 ENSMUSG00000020134 ENSMUSG00000075020 ENSMUSG00000026103 ENSMUSG00000078496 ENSMUSG00000047935 ENSMUSG00000024747 ENSMUSG00000033419 ENSMUSG00000009614 ENSMUSG00000032120 ENSMUSG00000040722 ENSMUSG00000039270 ENSMUSG00000026203 ENSMUSG00000066456 ENSMUSG00000028910 ENSMUSG00000044352 ENSMUSG00000073910 19.17 2.52 22.87 17.04 35.79 2.81 19.42 10.67 5.76 3.07 13.63 6.06 46.74 7.39 35.97 1.12 5.43 54.36 0.96 32.33 7.04 2.17 9.44 9.58 0.88 6.46 2.34 20.73 8.10 8.31 34.12 31.09 18.84 2.85 13.36 4.82 12.27 4.28 7.36 40.36 2.08 1.01 5.37 7.57 15.45 9.49 34.04 7.13 14.99 3.08 46.55 6.09 56.15 41.75 87.59 6.74 46.86 25.51 13.68 7.23 32.32 14.59 110.92 17.53 84.09 2.63 12.72 126.61 2.22 74.76 16.12 4.95 21.66 21.92 2.03 14.50 5.40 46.22 17.78 18.41 75.71 68.61 41.24 6.22 29.19 10.40 26.70 9.30 15.96 87.36 4.50 2.16 11.66 16.15 33.12 20.34 72.23 15.31 32.44 6.54 Development • Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean feature ID fold change FDR Pvalue ensembl gene id Prox1 rpkm mean C57 rpkm mean Sptan1 Dst Efcab2 Klhl5 Zbtb8b Ipo8 Reep2 Kcnj12 Prx Fah Nedd4l Vldlr Cpt2 Prkab2 Pcsk6 Ass1 Cyp7b1 Mthfd1l Gpx1 Uchl1 Eif2s3y A430105I19Rik Spag5 Cul3 Nudt17 Me1 Zfyve21 Gm14326 -‐2.8 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.7 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 4.7E-‐22 1.6E-‐06 2.7E-‐14 4.5E-‐20 1.3E-‐24 2.2E-‐22 1.8E-‐28 2.9E-‐24 6.6E-‐18 8.3E-‐09 3.3E-‐19 2.3E-‐17 5.7E-‐17 2.5E-‐15 3.6E-‐08 5.1E-‐14 1E-‐10 1.5E-‐27 8.9E-‐19 4.1E-‐18 1.4E-‐06 2.3E-‐23 4.2E-‐23 1.4E-‐22 3.1E-‐06 2.4E-‐15 1.6E-‐21 2.6E-‐05 ENSMUSG00000057738 ENSMUSG00000026131 ENSMUSG00000026495 ENSMUSG00000054920 ENSMUSG00000048485 ENSMUSG00000040029 ENSMUSG00000038555 ENSMUSG00000042529 ENSMUSG00000053198 ENSMUSG00000030630 ENSMUSG00000024589 ENSMUSG00000024924 ENSMUSG00000028607 ENSMUSG00000038205 ENSMUSG00000030513 ENSMUSG00000076441 ENSMUSG00000039519 ENSMUSG00000040675 ENSMUSG00000063856 ENSMUSG00000029223 ENSMUSG00000069049 ENSMUSG00000045838 ENSMUSG00000002055 ENSMUSG00000004364 ENSMUSG00000028100 ENSMUSG00000032418 ENSMUSG00000021286 ENSMUSG00000078862 65.64 6.80 5.04 5.85 7.08 9.64 12.41 10.15 13.87 1.35 2.52 7.24 15.80 7.45 1.74 4.36 3.00 14.37 165.58 57.91 6.74 4.80 17.91 52.92 1.18 4.99 19.62 1.34 140.46 14.68 10.57 12.29 15.03 20.52 26.31 21.47 29.09 2.87 5.28 15.08 32.74 15.35 3.53 8.88 6.14 29.63 337.66 117.93 13.57 9.77 36.48 107.96 2.50 10.06 39.89 2.65 Mettl22 Ncoa7 C77080 Rbp3 Spg20 Slc25a22 Trim9 Eno3 Tubb6 Mllt11 9930104L06Rik Gm14296 Spink13 Epb4.1l4a Rhot1 Osgin2 Dnajb1 Slc38a5 Mapk8ip1 Fktn Inf2 Tdrkh Pkp2 Kat2b Gabrg3 Mthfsl Dpf3 Arhgap31 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.6 -‐2.5 -‐2.5 -‐2.5 -‐2.5 -‐2.5 -‐2.5 -‐2.5 -‐2.5 -‐2.5 -‐2.5 -‐2.5 3.2E-‐13 1.8E-‐15 1.4E-‐20 7.9E-‐13 1.1E-‐22 1.2E-‐11 1.3E-‐23 3.7E-‐25 2.4E-‐22 6.2E-‐08 7.9E-‐20 8E-‐17 0.01804 5.3E-‐22 5.2E-‐15 3.9E-‐17 5E-‐10 5.8E-‐06 4.3E-‐24 9.6E-‐19 4.8E-‐07 2.9E-‐21 2.7E-‐27 3.3E-‐14 3.2E-‐06 7.9E-‐07 2.1E-‐08 2.8E-‐07 ENSMUSG00000039345 ENSMUSG00000039697 ENSMUSG00000050390 ENSMUSG00000041534 ENSMUSG00000036580 ENSMUSG00000019082 ENSMUSG00000021071 ENSMUSG00000060600 ENSMUSG00000001473 ENSMUSG00000053192 ENSMUSG00000044730 ENSMUSG00000074527 ENSMUSG00000073551 ENSMUSG00000024376 ENSMUSG00000017686 ENSMUSG00000041153 ENSMUSG00000005483 ENSMUSG00000031170 ENSMUSG00000027223 ENSMUSG00000028414 ENSMUSG00000037679 ENSMUSG00000041912 ENSMUSG00000041957 ENSMUSG00000000708 ENSMUSG00000055026 ENSMUSG00000079427 ENSMUSG00000021221 ENSMUSG00000022799 3.10 7.08 8.67 5.42 19.89 4.38 5.85 23.84 32.95 2.64 3.71 2.04 2.41 40.29 8.28 4.46 28.72 1.02 8.88 11.92 1.74 11.96 7.07 4.50 1.06 1.19 2.28 7.33 6.24 14.23 17.45 10.79 39.91 8.76 11.71 47.99 65.97 5.22 7.41 4.06 4.69 79.89 16.29 8.83 56.13 2.05 17.51 23.47 3.36 23.48 13.91 8.76 2.03 2.36 4.37 14.35 Development • Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information feature ID fold change FDR Pvalue ensembl gene id Calb1 Ppp1r14c Cngb3 Pde11a Tnc Hpse Rgs6 Gm12901 Sox21 C1qtnf4 Prokr1 Klf5 Tlr5 Slc1a2 Tff2 Slc44a5 Gm5900 Ttr Trac Gm15631 Pxdc1 Smim1 Tnnt3 Cxcl14 Cma1 Depdc7 Capn6 Ppfibp2 Wfikkn2 Pltp Trim6 Krt15 Srpx Gm10800 Itga8 Eln Phactr1 Tifa Tshr Gm10801 Col1a1 Mapk4 Nnat Nrg1 Col14a1 A930003A15Rik Fosl2 Gprc5a Pdlim3 Sytl2 120.5 67.6 55.9 49.5 30.6 27.0 20.8 18.6 18.4 18.1 13.4 12.7 12.5 12.0 11.9 11.5 10.5 10.2 10.1 10.0 8.5 7.9 7.7 7.7 7.7 7.6 7.6 7.5 7.2 7.2 7.2 7.1 6.6 6.4 6.4 6.4 6.2 6.2 6.2 6.1 6.1 6.1 5.6 5.6 5.6 5.6 5.5 5.5 5.5 5.5 1.1E-‐124 1.4E-‐77 2.3E-‐159 2.0E-‐34 1.2E-‐82 9.7E-‐82 7.3E-‐76 2.0E-‐02 3.8E-‐34 3.9E-‐45 1.6E-‐60 4.4E-‐10 9.9E-‐23 1.5E-‐78 2.7E-‐11 8.0E-‐49 5.5E-‐11 2.7E-‐03 3.0E-‐07 7.5E-‐11 1.4E-‐30 3.9E-‐45 5.7E-‐15 2.0E-‐17 3.5E-‐07 3.4E-‐15 2.0E-‐17 1.1E-‐44 6.7E-‐35 4.6E-‐15 3.5E-‐25 3.3E-‐05 2.1E-‐22 1.2E-‐02 2.8E-‐21 5.4E-‐04 1.2E-‐21 2.1E-‐23 8.4E-‐23 1.2E-‐02 1.2E-‐05 1.3E-‐37 1.2E-‐53 3.6E-‐12 2.8E-‐04 6.2E-‐27 5.2E-‐22 1.3E-‐14 3.5E-‐10 2.6E-‐17 ENSMUSG00000028222 ENSMUSG00000040653 ENSMUSG00000056494 ENSMUSG00000075270 ENSMUSG00000028364 ENSMUSG00000035273 ENSMUSG00000021219 ENSMUSG00000083720 ENSMUSG00000061517 ENSMUSG00000040794 ENSMUSG00000049409 ENSMUSG00000005148 ENSMUSG00000079164 ENSMUSG00000005089 ENSMUSG00000024028 ENSMUSG00000028360 ENSMUSG00000094685 ENSMUSG00000061808 ENSMUSG00000076928 ENSMUSG00000085067 ENSMUSG00000021411 ENSMUSG00000078350 ENSMUSG00000061723 ENSMUSG00000021508 ENSMUSG00000022225 ENSMUSG00000027173 ENSMUSG00000067276 ENSMUSG00000036528 ENSMUSG00000044177 ENSMUSG00000017754 ENSMUSG00000072244 ENSMUSG00000054146 ENSMUSG00000090084 ENSMUSG00000075014 ENSMUSG00000026768 ENSMUSG00000029675 ENSMUSG00000054728 ENSMUSG00000046688 ENSMUSG00000020963 ENSMUSG00000075015 ENSMUSG00000001506 ENSMUSG00000024558 ENSMUSG00000067786 ENSMUSG00000062991 ENSMUSG00000022371 ENSMUSG00000075330 ENSMUSG00000029135 ENSMUSG00000046733 ENSMUSG00000031636 ENSMUSG00000030616 Prox1 mean RPKM 11.89 12.28 18.91 2.01 55.12 11.58 5.46 22.89 3.51 21.80 26.03 2.05 2.11 7.35 5.02 4.76 3.23 5.00 2.70 3.08 10.77 5.10 3.82 4.21 2.03 2.43 11.99 10.21 5.88 11.76 8.35 8.79 5.70 956.81 3.40 9.16 2.52 10.42 5.02 269.14 102.48 5.85 40.59 3.63 6.36 53.49 4.29 3.58 3.84 2.21 C57 mean RPKM 0.08 0.14 0.26 0.03 1.40 0.33 0.21 0.93 0.15 0.94 1.51 0.12 0.13 0.48 0.33 0.33 0.24 0.40 0.19 0.24 0.99 0.51 0.38 0.42 0.21 0.25 1.26 1.08 0.63 1.30 0.91 0.97 0.67 124.16 0.42 1.13 0.32 1.31 0.64 36.60 13.25 0.75 5.63 0.51 0.90 7.37 0.61 0.51 0.54 0.32 feature ID fold change FDR Pvalue ensembl gene id Lox Mrc2 Gfra2 Gm11650 Slc22a5 Kera Rgs13 Glb1l2 Elmod1 Krt5 Klhl14 Gm21738 Slc11a1 Kcna5 4930426D05Rik Smoc2 Vcan Col17a1 Pdgfc Bves Ahnak Nkain4 Matn4 Ramp3 Lypd6b Cx3cl1 Tyr Klhdc8a Nfix Osbpl3 Hist1h1d Sox9 Rlbp1 Dsp Cldn11 Egfl6 Col8a1 Col12a1 Agtr2 Fras1 Dusp4 Frem1 Kitl Abcc4 Clec11a Crb1 Slc4a5 Sema3c Fam46a Ndnf 5.4 5.3 5.3 5.3 5.2 5.2 5.2 5.2 5.2 5.2 5.2 5.2 5.1 5.0 5.0 5.0 4.9 4.8 4.7 4.7 4.7 4.7 4.7 4.6 4.6 4.6 4.5 4.5 4.5 4.4 4.4 4.4 4.4 4.4 4.4 4.4 4.3 4.3 4.3 4.3 4.3 4.3 4.3 4.2 4.2 4.2 4.2 4.2 4.2 4.1 2.1E-‐04 2.1E-‐24 2.4E-‐34 2.6E-‐07 3.4E-‐35 2.6E-‐03 6.3E-‐14 3.7E-‐27 1.2E-‐13 3.3E-‐04 1.8E-‐20 3.8E-‐02 1.0E-‐18 3.3E-‐11 1.1E-‐09 7.1E-‐04 4.3E-‐15 9.6E-‐04 7.0E-‐13 4.8E-‐18 2.6E-‐06 5.9E-‐17 7.7E-‐03 4.0E-‐17 3.5E-‐13 2.2E-‐43 3.5E-‐05 7.5E-‐13 2.9E-‐04 8.6E-‐46 1.2E-‐03 8.8E-‐28 9.0E-‐07 1.0E-‐04 1.3E-‐04 1.1E-‐03 6.0E-‐04 5.2E-‐04 4.8E-‐03 7.3E-‐14 3.2E-‐29 3.2E-‐08 3.5E-‐23 9.6E-‐33 1.4E-‐12 6.6E-‐12 1.6E-‐04 3.0E-‐04 2.0E-‐09 2.2E-‐16 ENSMUSG00000024529 ENSMUSG00000020695 ENSMUSG00000022103 ENSMUSG00000087184 ENSMUSG00000018900 ENSMUSG00000019932 ENSMUSG00000051079 ENSMUSG00000036395 ENSMUSG00000041986 ENSMUSG00000061527 ENSMUSG00000042514 ENSMUSG00000095280 ENSMUSG00000026177 ENSMUSG00000045534 ENSMUSG00000043168 ENSMUSG00000023886 ENSMUSG00000021614 ENSMUSG00000025064 ENSMUSG00000028019 ENSMUSG00000071317 ENSMUSG00000069833 ENSMUSG00000027574 ENSMUSG00000016995 ENSMUSG00000041046 ENSMUSG00000026765 ENSMUSG00000031778 ENSMUSG00000004651 ENSMUSG00000042115 ENSMUSG00000001911 ENSMUSG00000029822 ENSMUSG00000052565 ENSMUSG00000000567 ENSMUSG00000039194 ENSMUSG00000054889 ENSMUSG00000037625 ENSMUSG00000000402 ENSMUSG00000068196 ENSMUSG00000032332 ENSMUSG00000068122 ENSMUSG00000034687 ENSMUSG00000031530 ENSMUSG00000059049 ENSMUSG00000019966 ENSMUSG00000032849 ENSMUSG00000004473 ENSMUSG00000063681 ENSMUSG00000068323 ENSMUSG00000028780 ENSMUSG00000032265 ENSMUSG00000049001 Prox1 mean RPKM 13.32 21.66 13.70 2.23 14.78 8.77 15.63 4.35 3.17 15.57 4.10 43.94 5.44 7.30 3.46 8.17 18.68 2.32 6.07 6.48 10.79 10.71 4.47 6.87 4.15 94.65 15.38 2.68 2.30 12.89 4.88 12.97 8.25 3.32 4.01 3.86 8.19 10.04 7.46 9.69 20.67 2.28 19.30 20.38 3.71 2.40 8.44 2.74 4.50 13.13 C57 mean RPKM 1.98 3.24 2.02 0.33 2.21 1.26 2.33 0.65 0.48 2.42 0.62 7.16 0.84 1.16 0.54 1.27 3.04 0.39 1.02 1.07 1.86 1.79 0.74 1.16 0.70 15.90 2.73 0.46 0.41 2.28 0.86 2.31 1.50 0.61 0.72 0.69 1.53 1.89 1.38 1.80 3.72 0.42 3.60 3.78 0.69 0.44 1.61 0.51 0.84 2.53 Development • Supplementary information Supplementary Table 4: Genes up-‐regulated following Prox1 loss feature ID Fam46a Ndnf Papss2 Hist1h1b Asic2 Spp1 Kdelr3 Osr2 Postn Dab2 Npr3 Clec14a Tspan10 Fbln5 Col6a1 Aqp4 Acta2 Lpcat2 Col16a1 Dcn Col6a2 Pmel Col1a2 Apoc1 Wnt6 Kctd12b Tnik Tgfbi Gli1 Enc1 Slc7a7 Pipox Gpnmb Slc24a5 Trp53i11 Tyrp1 Slc6a11 Zfhx3 Fat3 Fst Lrrn2 Pex5l Cpa3 Igfbp2 Steap4 Wisp1 Rab32 Jam2 Zfp462 fold change 4.2 4.1 4.1 4.1 4.1 4.0 4.0 4.0 3.9 3.9 3.9 3.9 3.8 3.8 3.8 3.8 3.8 3.8 3.8 3.7 3.7 3.7 3.7 3.7 3.7 3.7 3.7 3.6 3.6 3.6 3.6 3.6 3.6 3.6 3.6 3.5 3.5 3.5 3.5 3.5 3.5 3.5 3.5 3.5 3.5 3.5 3.4 3.4 3.4 FDR Pvalue 2.0E-‐09 2.2E-‐16 4.1E-‐12 1.6E-‐02 6.3E-‐12 6.5E-‐08 4.3E-‐08 3.1E-‐02 1.1E-‐04 2.6E-‐21 3.8E-‐15 3.1E-‐25 1.1E-‐05 2.3E-‐03 1.4E-‐04 1.1E-‐11 1.6E-‐29 9.0E-‐12 2.2E-‐04 2.9E-‐05 3.8E-‐04 3.0E-‐04 3.6E-‐05 9.0E-‐04 4.1E-‐02 3.2E-‐21 1.1E-‐25 5.7E-‐05 5.6E-‐09 1.6E-‐30 2.2E-‐24 8.8E-‐10 8.0E-‐05 2.1E-‐04 3.1E-‐21 3.9E-‐04 4.5E-‐20 8.6E-‐07 1.1E-‐11 5.9E-‐09 1.2E-‐15 1.2E-‐13 6.7E-‐05 2.4E-‐15 2.2E-‐07 4.8E-‐03 4.9E-‐12 5.2E-‐35 2.9E-‐14 ensembl gene id Prox1 mean RPKM ENSMUSG00000032265 ENSMUSG00000049001 ENSMUSG00000024899 ENSMUSG00000058773 ENSMUSG00000020704 ENSMUSG00000029304 ENSMUSG00000010830 ENSMUSG00000022330 ENSMUSG00000027750 ENSMUSG00000022150 ENSMUSG00000022206 ENSMUSG00000045930 ENSMUSG00000039691 ENSMUSG00000021186 ENSMUSG00000001119 ENSMUSG00000024411 ENSMUSG00000035783 ENSMUSG00000033192 ENSMUSG00000040690 ENSMUSG00000019929 ENSMUSG00000020241 ENSMUSG00000025359 ENSMUSG00000029661 ENSMUSG00000040564 ENSMUSG00000033227 ENSMUSG00000041633 ENSMUSG00000027692 ENSMUSG00000035493 ENSMUSG00000025407 ENSMUSG00000041773 ENSMUSG00000000958 ENSMUSG00000017453 ENSMUSG00000029816 ENSMUSG00000035183 ENSMUSG00000068735 ENSMUSG00000005994 ENSMUSG00000030307 ENSMUSG00000038872 ENSMUSG00000074505 ENSMUSG00000021765 ENSMUSG00000026443 ENSMUSG00000027674 ENSMUSG00000001865 ENSMUSG00000039323 ENSMUSG00000012428 ENSMUSG00000005124 ENSMUSG00000019832 ENSMUSG00000053062 ENSMUSG00000060206 4.50 13.13 4.68 7.35 2.55 10.54 6.36 2.86 8.06 12.26 13.31 12.31 10.15 3.14 17.74 2.65 20.86 2.79 3.22 37.46 9.32 126.72 49.37 2.22 3.12 13.89 3.83 9.09 7.53 22.17 26.13 5.95 16.18 4.03 28.17 16.22 11.66 12.64 10.32 8.80 5.71 2.40 4.20 118.60 4.25 2.08 9.94 9.86 20.46 C57 mean RPKM 0.84 2.53 0.90 1.44 0.49 2.03 1.24 0.57 1.63 2.48 2.74 2.49 2.10 0.65 3.68 0.54 4.27 0.58 0.68 7.82 1.98 27.29 10.60 0.45 0.69 3.00 0.81 1.99 1.62 4.83 5.62 1.27 3.59 0.89 6.25 3.65 2.53 2.88 2.32 1.98 1.27 0.54 0.95 26.93 0.96 0.48 2.26 2.24 4.80 feature ID Edaradd Dct Slc45a2 Cacna1g Tmem144 Bace2 Plxnc1 Hs3st5 Col8a2 Creb3l1 Tmem169 Frk Nid2 Pqlc2 Aass Igsf3 Mlana Krt19 Pdgfrl 4932443I19Rik Myof Sfrp2 2010107G23Rik Satb2 Cdh3 Cacng4 Prrx1 Tmem35 Fjx1 Emp2 Flnc Nfia Vcam1 Mmp14 Tril Anpep Sema3f Sncaip Egfem1 Slc35d3 Tmem119 Lars2 Pcdh9 Tst Cd44 Hs3st6 Slc38a8 Igf1 fold change 3.4 3.4 3.4 3.4 3.4 3.3 3.3 3.3 3.3 3.3 3.3 3.3 3.3 3.3 3.3 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.0 3.0 FDR Pvalue 9.5E-‐19 3.8E-‐04 7.6E-‐04 1.7E-‐04 6.8E-‐07 1.3E-‐04 2.1E-‐17 3.2E-‐12 2.1E-‐04 4.8E-‐04 7.7E-‐09 8.6E-‐07 4.7E-‐17 1.1E-‐14 2.7E-‐09 6.5E-‐26 4.5E-‐05 1.4E-‐03 9.9E-‐06 7.5E-‐05 3.0E-‐05 2.3E-‐16 2.3E-‐15 5.3E-‐11 1.9E-‐04 1.4E-‐33 1.1E-‐04 2.0E-‐17 6.5E-‐30 6.7E-‐10 2.8E-‐04 8.9E-‐06 1.5E-‐03 3.5E-‐20 1.8E-‐06 6.4E-‐05 1.2E-‐22 6.1E-‐04 8.2E-‐21 1.1E-‐04 9.7E-‐04 6.0E-‐03 5.5E-‐05 2.4E-‐18 2.4E-‐03 6.6E-‐07 2.6E-‐03 3.5E-‐05 ensembl gene id Prox1 mean RPKM C57 mean RPKM ENSMUSG00000095105 ENSMUSG00000022129 ENSMUSG00000022243 ENSMUSG00000020866 ENSMUSG00000027956 ENSMUSG00000040605 ENSMUSG00000074785 ENSMUSG00000044499 ENSMUSG00000056174 ENSMUSG00000027230 ENSMUSG00000026188 ENSMUSG00000019779 ENSMUSG00000021806 ENSMUSG00000028744 ENSMUSG00000029695 ENSMUSG00000042035 ENSMUSG00000024806 ENSMUSG00000020911 ENSMUSG00000031595 ENSMUSG00000090336 ENSMUSG00000048612 ENSMUSG00000027996 ENSMUSG00000020083 ENSMUSG00000038331 ENSMUSG00000061048 ENSMUSG00000020723 ENSMUSG00000026586 ENSMUSG00000033578 ENSMUSG00000075012 ENSMUSG00000022505 ENSMUSG00000068699 ENSMUSG00000028565 ENSMUSG00000027962 ENSMUSG00000000957 ENSMUSG00000043496 ENSMUSG00000039062 ENSMUSG00000034684 ENSMUSG00000024534 ENSMUSG00000063600 ENSMUSG00000050473 ENSMUSG00000054675 ENSMUSG00000035202 ENSMUSG00000055421 ENSMUSG00000044986 ENSMUSG00000005087 ENSMUSG00000039628 ENSMUSG00000034224 ENSMUSG00000020053 11.46 43.86 2.58 3.77 2.56 3.51 7.03 2.48 15.05 3.89 2.61 2.20 42.06 5.50 3.16 22.18 16.25 2.77 2.27 2.78 2.12 662.84 8.35 2.03 6.39 31.51 5.04 40.16 29.87 2.83 3.75 4.13 5.64 62.64 13.10 2.69 20.57 3.07 20.82 2.21 5.63 11537.92 2.60 24.53 2.66 6.10 21.71 4.18 2.63 10.43 0.61 0.90 0.60 0.83 1.67 0.58 3.61 0.93 0.62 0.52 10.28 1.32 0.77 5.36 3.97 0.67 0.54 0.68 0.52 164.28 2.06 0.50 1.61 7.82 1.28 9.87 7.43 0.71 0.98 1.07 1.45 16.14 3.43 0.69 5.28 0.80 5.31 0.56 1.47 3080.25 0.67 6.29 0.69 1.58 5.79 1.12 Development • Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information Development 143: doi:10.1242/dev.127860: Supplementary information Col13a1 Col9a2 Lpl Ldhb Vash2 Dnm1 Col25a1 Cxcl12 Thbs2 Car14 Lum Calml3 Egfr Nes Cd83 Rgma Mt2 Gm26917 Dkk2 Ror2 5730559C18Rik Pla2g4a 2700069I18Rik Mid2 Krt18 AY036118 Rbm20 Bdh2 Fam101b Chd3 Gm14236 Mreg Ddr2 Ntrk2 Olfml1 S100a1 C230034O21Rik Tenm4 Dmp1 Ccdc177 Sall2 Gzmm Rab27a Antxr1 Twist1 Cdo1 fold change 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 2.9 2.9 2.9 2.9 2.9 2.9 2.9 2.9 2.9 2.9 2.9 2.9 2.9 2.8 2.8 2.8 2.8 2.8 2.8 2.8 2.8 2.8 2.8 2.8 2.8 2.8 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 FDR Pvalue 4.9E-‐38 5.4E-‐14 1.0E-‐25 2.0E-‐18 7.3E-‐28 6.3E-‐04 1.0E-‐04 2.2E-‐03 2.9E-‐04 3.6E-‐16 6.2E-‐05 9.9E-‐03 8.0E-‐04 5.1E-‐24 5.5E-‐06 1.8E-‐10 3.1E-‐04 4.8E-‐03 7.5E-‐04 2.2E-‐05 5.6E-‐07 6.7E-‐27 2.6E-‐05 5.7E-‐10 1.3E-‐05 7.7E-‐03 2.9E-‐08 2.8E-‐05 4.3E-‐20 1.5E-‐10 9.7E-‐03 8.7E-‐07 3.0E-‐04 3.0E-‐14 4.2E-‐02 1.5E-‐06 3.5E-‐02 8.5E-‐05 2.5E-‐02 2.5E-‐09 2.8E-‐18 1.5E-‐03 1.8E-‐04 1.1E-‐24 1.2E-‐02 5.1E-‐07 ensembl gene id Prox1 mean RPKM C57 mean RPKM ENSMUSG00000058806 ENSMUSG00000028626 ENSMUSG00000015568 ENSMUSG00000030246 ENSMUSG00000037568 ENSMUSG00000026825 ENSMUSG00000058897 ENSMUSG00000061353 ENSMUSG00000023885 ENSMUSG00000038526 ENSMUSG00000036446 ENSMUSG00000063130 ENSMUSG00000020122 ENSMUSG00000004891 ENSMUSG00000015396 ENSMUSG00000070509 ENSMUSG00000031762 ENSMUSG00000097971 ENSMUSG00000028031 ENSMUSG00000021464 ENSMUSG00000041605 ENSMUSG00000056220 ENSMUSG00000086224 ENSMUSG00000000266 ENSMUSG00000023043 ENSMUSG00000045999 ENSMUSG00000043639 ENSMUSG00000028167 ENSMUSG00000020846 ENSMUSG00000018474 ENSMUSG00000086411 ENSMUSG00000039395 ENSMUSG00000026674 ENSMUSG00000055254 ENSMUSG00000051041 ENSMUSG00000044080 ENSMUSG00000086181 ENSMUSG00000048078 ENSMUSG00000029307 ENSMUSG00000062961 ENSMUSG00000049532 ENSMUSG00000054206 ENSMUSG00000032202 ENSMUSG00000033420 ENSMUSG00000035799 ENSMUSG00000033022 21.61 28.97 13.47 81.89 25.76 3.74 2.06 4.66 3.84 35.73 75.36 3.47 2.80 124.95 3.53 6.91 5.68 4097.06 24.01 3.52 5.89 7.70 3.38 3.29 21.26 175.12 2.16 10.74 16.16 27.76 207.37 3.57 5.51 9.05 2.42 8.40 2.77 8.47 22.74 2.95 43.54 2.93 5.86 67.56 10.59 12.86 5.55 7.50 3.52 21.44 6.77 1.00 0.55 1.28 1.01 9.55 20.41 0.94 0.77 33.66 0.94 1.86 1.52 1152.77 6.61 0.97 1.63 2.09 0.93 0.90 6.01 50.59 0.60 3.02 4.52 7.93 60.61 1.01 1.59 2.54 0.70 2.39 0.78 2.46 6.84 0.85 12.57 0.84 1.72 19.41 3.10 3.72 feature ID Maml2 Col3a1 Smim24 Stbd1 Sepp1 Nupr1 Rnf165 Sertad4 Lama4 Prkcb Sh3pxd2a Irx5 Hif3a Slc1a3 Creb3l2 Akr1b10 Ntf3 Fez1 Efemp1 Slc9a3r1 Prom1 Dok1 Apod Dgkh Itpr3 Jph2 Lingo1 Cryl1 Gm4524 Mtcl1 Olfml3 Crabp2 Adam19 Anxa2 Slc6a15 Clmp Sparcl1 Fbln2 Col11a1 Paqr4 Optc Clip1 Shank1 Fzd8 Trib2 fold change 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 FDR Pvalue 4.5E-‐19 7.8E-‐04 1.6E-‐03 2.7E-‐08 2.3E-‐11 2.2E-‐11 1.9E-‐17 2.0E-‐03 1.6E-‐09 3.0E-‐06 9.7E-‐08 4.8E-‐03 3.1E-‐10 3.1E-‐08 9.4E-‐15 1.7E-‐05 2.4E-‐03 2.9E-‐17 4.1E-‐04 2.7E-‐11 5.3E-‐16 2.3E-‐09 7.5E-‐04 1.2E-‐03 1.8E-‐05 2.1E-‐09 8.9E-‐11 2.4E-‐05 1.0E-‐12 4.2E-‐20 1.8E-‐10 7.1E-‐06 7.0E-‐04 1.3E-‐12 8.6E-‐04 3.6E-‐09 4.5E-‐14 8.9E-‐04 3.3E-‐03 8.3E-‐08 3.6E-‐02 6.1E-‐16 6.7E-‐08 1.5E-‐07 1.1E-‐23 ensembl gene id ENSMUSG00000031925 ENSMUSG00000026043 ENSMUSG00000078439 ENSMUSG00000047963 ENSMUSG00000064373 ENSMUSG00000030717 ENSMUSG00000025427 ENSMUSG00000016262 ENSMUSG00000019846 ENSMUSG00000052889 ENSMUSG00000053617 ENSMUSG00000031737 ENSMUSG00000004328 ENSMUSG00000005360 ENSMUSG00000038648 ENSMUSG00000061758 ENSMUSG00000049107 ENSMUSG00000032118 ENSMUSG00000020467 ENSMUSG00000020733 ENSMUSG00000029086 ENSMUSG00000068335 ENSMUSG00000022548 ENSMUSG00000034731 ENSMUSG00000042644 ENSMUSG00000017817 ENSMUSG00000049556 ENSMUSG00000021947 ENSMUSG00000090257 ENSMUSG00000052105 ENSMUSG00000027848 ENSMUSG00000004885 ENSMUSG00000011256 ENSMUSG00000032231 ENSMUSG00000019894 ENSMUSG00000032024 ENSMUSG00000029309 ENSMUSG00000064080 ENSMUSG00000027966 ENSMUSG00000023909 ENSMUSG00000010311 ENSMUSG00000049550 ENSMUSG00000038738 ENSMUSG00000036904 ENSMUSG00000020601 Prox1 mean RPKM 16.26 46.23 2.92 6.27 62.12 116.88 13.72 3.32 13.31 2.59 15.55 2.93 7.63 6.45 27.83 2.06 3.96 16.29 11.52 28.26 23.87 8.51 2.39 2.33 2.70 4.07 4.10 3.49 16.01 22.25 30.96 99.87 2.88 33.43 17.03 7.36 57.05 6.29 6.04 6.13 6.11 12.94 4.81 4.12 22.21 C57 mean RPKM 4.73 13.96 0.86 1.83 18.56 33.45 4.03 0.99 4.01 0.76 4.66 0.86 2.26 1.92 8.35 0.62 1.17 4.87 3.47 8.55 7.23 2.57 0.72 0.70 0.83 1.23 1.24 1.05 4.81 6.82 9.23 30.97 0.91 10.37 5.32 2.29 17.89 1.98 1.92 1.91 1.85 4.08 1.51 1.30 6.98 Development • Supplementary information feature ID
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