Supplemental Table 1. Top transcription factors/regulators predicted to be responsible for the global gene expression changes caused by Gremlin1 knockdown.

p-values IN528, IN528, 3691, 3691, shGrem1 shGrem1 shGrem1 shGrem1 Regulator Activation 485 2456 485 2456 Average CDKN1A Activated 4.75E-37 1.61E-37 2.56E-44 4.75E-37 2.78E-37 let-7 Activated 3.88E-21 2.43E-21 9.25E-20 3.88E-21 2.57E-20 RB1 Activated 1.17E-19 2.84E-21 1.86E-22 1.17E-19 5.93E-20 TP53 Activated 3.03E-19 2.63E-22 4.64E-28 3.03E-19 1.52E-19 VEGF Inhibited 2.57E-17 6.24E-18 1.22E-20 2.57E-17 1.44E-17 CCND1 Inhibited 3.23E-17 7.69E-19 1.18E-21 3.23E-17 1.63E-17 CDK4 Inhibited 4.64E-17 6.22E-19 3.56E-21 4.64E-17 2.34E-17 ERBB2 Inhibited 3.36E-16 6.67E-19 1.99E-21 3.36E-16 1.68E-16 NUPR1 Activated 1.07E-15 1.11E-15 3.44E-15 1.07E-15 1.67E-15 E2F1 Inhibited 2.67E-20 4.15E-18 9.62E-15 2.67E-20 2.41E-15 HGF Inhibited 6.50E-15 7.37E-19 1.29E-22 6.50E-15 3.25E-15 CDKN2A Activated 8.66E-15 1.90E-16 1.67E-19 8.66E-15 4.38E-15 E2F4 Inhibited 5.40E-34 4.40E-32 3.89E-13 5.40E-34 9.73E-14 FOXM1 Inhibited 1.12E-10 1.09E-10 1.17E-17 1.12E-10 8.33E-11 RBL1 Activated 7.15E-09 1.45E-10 3.88E-11 7.15E-09 3.62E-09

Supplemental Table 2. RT-PCR primers used in this study

Gene Protein Directionality Sequence Actin Actin Forward 5’-ACCTTCTACAATGAGCTGCG-3’ Actin Actin Reverse 5’-CCTGGATAGCAACGTACATGG-3’ BMP2 BMP2 Forward 5’-CTACATGCTAGACCTGTATCGC-3’ BMP2 BMP2 Reverse 5’-CCCACTCGTTTCTGGTAGTTC-3’ BMP4 BMP4 Forward 5’-GCACTGGTCTTGAGTATCCTG-3’ BMP4 BMP4 Reverse 5’-TGCTGAGGTTAAAGAGGAAACG-3’ BMP7 BMP7 Forward 5’-CTGTATGTCAGCTTCCGAGAC-3’ BMP7 BMP7 Reverse 5’-CGTTCATGTAGGAGTTCAGAGG-3’ BMPR1A BMPR1a Forward 5’-CTGGGCCTTGCTGTTAAATTC-3’ BMPR1A BMPR1a Reverse 5’-GTAGGGCTGGAAGTGGTTTT-3’ BMPR1B BMPR1b Forward 5’-CTGCACAGAAAGGAACGAATG-3’ BMPR1B BMPR1b Reverse 5’-AGGACCAAGAGCAAACTACAG-3’ Chrd Chordin Forward 5’-TCCGCTTCTCTATCTCCTACAG-3’ Chrd Chordin Reverse 5’-GAGACAACCGAGGCACTG-3’ Chrdl1 Ventroptin Forward 5’-AGAAGTACAGAGTGGGTGAGAG-3’ Chrdl1 Ventroptin Reverse 5’-CACAGGAGAAAGGCAATGAAC-3’ GalC Galactosyl- Forward 5’-AATTATCAAGGTCTCCAGCGAG-3’ ceramidase GalC Galactosyl- Reverse 5’- CATCTTTTGCTGAATGGGTTCC-3’ ceramidase GAPDH GAPDH Forward 5’- GAAGGTGAAGGTCGGAGTC-3’ GAPDH GAPDH Reverse 5’- GAAGATGGTGATGGGATTTC-3’ GFAP GFAP Forward 5’-TGTGTGAGTAAGAAGGGACCGCAA-3’ GFAP GFAP Reverse 5’-GCAGGGCATGACTTGTCCCATTT-3’ Grem1 Gremlin1 Forward 5’-ATGAGCCGCACAGCCTACACG-3’ Grem1 Gremlin1 Reverse 5’-TTAATCCAAATCGATGGATATGC-3’ Map2 Map-2 Forward 5’- TGAGGTTGCCAGGAGGAAATCAGT-3’ Map2 Map-2 Reverse 5’- AGGTGATGGCAATGGGACTGTGTA-3’ Nog Noggin Forward 5’-CAGCACTATCTCCACATCCG-3’ Nog Noggin Reverse 5’-TCGTTCAGATCCTTTTCCTTGG-3’ Olig2 Olig2 Forward 5’-GGTAAGTGCGCAATGCTAAGCTGT-3’ Olig2 Olig2 Reverse 5’-TACAAAGCCCAGTTTGCAACGCAG-3’ S100b S100b Forward 5’-AGGGAGACAAGCACAAGCTGAAGA-3’ S100b S100b Reverse 5’-TGTCCACAACCTCCTGCTCTTTGA-3’ Sox2 Sox2 Forward 5’-CACACTGCCCCTCTCAC-3’ Sox2 Sox2 Reverse 5’-TCCATGCTGTTTCTTACTCTCC-3’ Tuj1 β3-tubulin Forward 5’- TCGTTGTCGATGCAGTAGGTCTCA-3’ Tuj1 β3-tubulin Reverse 5’- ATCAGCAAGGTGCGTGAGGAGTAT-3’ VWC2 Brorin Forward 5’-CCTGTGTACGAGCCTGATC-3’ VWC2 Brorin Reverse 5’-ATTCTCCATGTGCCTTCCTC-3’

Supplemental Table 3. Primers for TP53 amplification

Exon Directionality Sequence Exon 4 Forward 5’-CCTGGTCCTCTGACTGCTCTTTTCACCCA-3’ Exon 4 Reverse 5’-GGCCAGGCATTGAAGTCTCAT-3’ Exon 5 Forward 5’-CAACTCTGTCTCCTTCCT-3’ Exon 5 Reverse 5’-TGTCGTCTCTCCAGCCCC-3’ Exon 6 Forward 5’-AGAGACGACAGGGCTGGTTG-3’ Exon 6 Reverse 5’-CTTAACCCCTCCTCCCAGAG-3’ Exon 7 Forward 5’-CCTCATCTTGGGCCTGTGTT-3’ Exon 7 Reverse 5’-AGTGTGCAGGGTGGCAAGTG-3’ Exon 8 Forward 5’-CCTTACTGCCTCTTGCTTCT-3’ Exon 8 Reverse 5’-ATAACTGCACCCTTGGTCTC-3’ Exon 9 Forward 5’-GGAGACCAAGGGTGCAGTTATGCCTCAG-3’ Exon 9 Reverse 5’-CCCAATTGCAGGTAAAACAG-3’