Keywords: Supplementary Table S1, Primer sequences for semi-quantitative RT-PCR experiments, Gene Name Forward: 5'-3' (underline indicates NotI site) Reverse: 5'-3' (underline indicates XhoI site)

DEPDC1

GCTACAAGTAAAGAGGGGATGG GGACAGAAAGGTAAGTCAGTGGG 

ZNF224

GAGCAGCATGGGAAGAACAT TGAGGCCTGACTAAAGCACA 
IkBα TATATCCACACTGCACACTGC CCATTTACAGGAGGGTAACAC GAPDH CGACCACTTTGTCAAGCTCA GGTTGAGCACAGGGTACTTTATT
GAPDH (glyceraldehyde-3-phosphate dehydrogenase); a quantitative internal control. 

Harada Y., et al.

Supplementary Table S2. Sequences of primers used to generate expression vector constructs. 

Table S3 . Amino acids sequences of cell-permeable peptide.

 S3 
			Harada Y., et al.
	Construct Name Supplementary Peptide Name	Forward: 5'-3' (underline indicates NotI site) Amino-acid sequences	Reverse: 5'-3' (underline indicates XhoI site)
	ZNF224-FLAG 11R-DEP:598-615	GGAAAGCGGCCGCATGACCACGTTCAA RRRRRRRRRRR-GGG-AIDALQLCCLLLPPPNRR	GCCGCTCGAGAGGTTTTTCTCCAACATGAA
	DEPDC1 (1-147) 11R-DEP:611-628	ATTCGCGGCCGCGGATGGAGAGTCAGGGTGTG RRRRRRRRRRR-GGG-PPNRRKLQLLMRMISRMS	CCCGCTCGAGAGTTCTACGAGATAAGTTTCG
	DEPDC1 (1-300) 11R-DEP:624-641	ATTCGCGGCCGCGGATGGAGAGTCAGGGTGTG RRRRRRRRRRR-GGG-ISRMSQNVDMPKLHDAMG	CCCGCTCGAGTACAAATAATTCGTAATATTC
	DEPDC1 (177-597) 11R-DEP:636-653	ATTCGCGGCCGCTTGATAATAGAGAACTAAGCCA RRRRRRRRRRR-GGG-LHDAMGTRSLMIHTFSRC	CCCGCTCGAGAACCCTCTCTAAATGAGGTTG
	DEPDC1 (300-669) Scramble	ATTCGCGGCCGCACCATGGTAAACATTTTGGTTGTTTGTG RRRRRRRRRRR-GGG-LRMSRLSPNMIMQRPKRL	CCCGCTCGAGTCCAGCAAGAAGCTCATC
	DEPDC1 (587-740)	ATTCGCGGCCGCACCATGCAAAGCTTGCTGCAACCTCA	CCCGCTCGAGAGCTTGAGAGGTAGAAAC
	DEPDC1 (654-811)	ATTCGCGGCCGCACCATGTCTTACTTACAGACTGCAGTG	CCCGCTCGAGTCTTAGACTACGGAACTTTG

Supplementary TableS4. 
List of candidate down-stream genes regulated by the DEPDC1-ZNF224 complex

  
							Accession	BC
	si-DEPDC1 12h	si-DEPDC1 24h	si-ZNF224 12h	si-ZNF224 24h	Gene			
						Gene Name †	Number †	microarray
	(Cy5/Cy3 ratio)*	(Cy5/Cy3 ratio)*	(Cy5/Cy3 ratio)*	(Cy5/Cy3 ratio)*	symbol †			
								(cases) ‡
	1.03	2.51	1.36	1.63	CALM3	Calmodulin 3 (phosphorylase kinase, delta)	BC005137	27/36
	3.02	2.39	2.88	5.05	FSTL1	Follistatin-like 1	BC000050	16/16
	1.62	2.26	1.18	2.25	GLO1	Glyoxalase I	BC011365	12/41
	1.9	2.22	1.13	1.81	TNFAIP3	Tumor necrosis factor, alpha-induced protein 3 (A20)	Q60769	21/41
	1.52	1.88	1.57	1.81	DLG1	Discs, large homolog 1 (Drosophila)	U13897	8/14
	1.56	1.73	1.09	1.94	DUSP3	Dual specificity phosphatase 3	BC002682	37/41
	1.09	1.63	1.28	1.8	TGFBI	Transforming growth factor, beta-induced, 68kDa	BC013738	31/41
	1.34	1.63	1.06	1.59	TMEM43	Transmembrane protein 43	NM_024334	29/41
	1.63	1.56	1.07	1.79	TSC22D1	TSC22 domain family, member 1	BC000456	34/40

*We selected genes whose normalized expression ratios (Cy5/Cy3 ratio; si-DEPDC1 or si-ZNF224-transfected cells / si-EGFP-transfected cells) were >1.5 at 24 h after the transfection, and were also commonly down-regulated in bladder cancer microarray data reported previously (Reference 1 in Supplementary Methods). †Gene symbols, gene names and accession number were retrieved from the Unigene Database (build No. 131). ‡Bladder cancer (BC) microarray indicates number of cases with expression ratios >0.5 in informative bladder cancer cases (Reference 1 in Supplementary Methods).