Table 1. Selected data obtained during mass-spectrometry analyses of the proteome of cilia isolated from wild-type and mutant cells.

Protein name	Number in TGD	WT	CCDC113-KO	WT	CCDC96-coDel	WT	DRC3-coDel
Ccdc113	TTHERM_00312810	33/8	0	18/7	0	10/7	7/4
			0	13/10	0	13/10	5/4
Ccdc96	TTHERM_00529650	39/16	3/2	31/16	0	21/15	15/9
			0	21/12	0	21/12	8/7
Fap57A	TTHERM_00105300	14/7	15/9	13/9	22/14	7/6	13/10
			10/7	15/12	10/9	15/12	14/13
Actin	TTHERM_00190950	186/16	148/16	96/16	91/14	66/14	78/11
			86/15	65/16	59/18	65/16	54/14
Drc1	TTHERM_01345750	37/17	42/23 (1)	38/20	39/17	16/10	18/10
			24/18 (1)	25/15	18/12	25/15	10/9
Drc2	TTHERM_00971830	26/11	30/19	20/11	19/11	20/6	14/8
			18/13	8/7	10/8	8/7	2/2
Drc3	TTHERM_00316370	48/11	52/21	31/15	34/17	22/12	0
			32/16	21/12	17/10	21/12	0
Drc4a	TTHERM_00857910	30/15	39/17	32/15	46/17	29/10	14/10
			22/16	28/18	21/15	18/18	6/6
Drc4b	TTHERM_00649240	37/13	48/21	26/14	42/14	17/8	22/10
			26/15	20/11	11/7	20/11	5/4
Drc7	TTHERM_00473320	55/15	48/23	40/22	61/24	22/11	17/9
			37/20	27/18	31/18	27/18	13/12
RSP3B	TTHERM_00566810	58/18	81/26	32/12	71/18	36/12	20/8
			37/16	37/17	28/16	36/17	9/6
PF6	TTHERM_00430030	132/50	163/56	73/34	92/38	56/28	33/23
			88/41	51/32	44/26	51/32	37/26
Cfap251	TTHERM_01262850	39/14	25/13	36/16	56/26	32/17	15/9
			27/15	32/21	29/19	32/21	17/11
Cfap299	TTHERM_00427460	22/7	2/2	13/5	0	4/3	4/2
			0	6/4	0	6/4	3/3

Table shows the numbers (X/Y) of all the identified peptides (X, in a Mascot program, all significant matches) and unique peptide sequences (Y, in a Mascot program, significant sequences). Data in two rows represent data from two independent experiments (complete data are presented in S2–S4 Tables). Note that Ccdc113 is missing in CCDC96-coDel mutants and Ccdc96 is missing in cilia isolated from CCDC113-KO cells and that both Ccdc96 and Ccdc113 are present in cilia of DRC3-coDel mutant. One of the control samples (WT) was common for CCDC96-coDel and DCR3-coDel mutants. The ortholog of Chlamydomonas FBB9 (flagellar/basal body protein 9) and mammalian Cfap299 was also reduced or missing in CCDC113-KO and CCDC96-coDel mutants but this protein was not identified among ciliary proteins co-immunoprecipitating with Ccdc113 or biotinylated in cells expressing Ccdc96-HA-BirA* or Ccdc113-HA-BirA* (see S5–S7 Tables). Radial spoke protein Rsp3B and central apparatus protein Pf6 data are shown to compare the amount of proteins in different samples. TGD–Tetrahymena Genome Database.