Table I. Comparison of peptide data quality for RNA polymerase II subunits.

All known RNA polymerase II subunits (Pol2A–Pol2L) except Pol2F were identified and quantified in the SILAC co-IP using GFP-Pol2C as bait. They all show high sequence coverage and a large number of peptides identified and quantified, underlining the quality of the data. The bait protein, GFP-Pol2C, is bold. log₂(H/M) ratios of all subunits are normalized in the table so that log₂(H/M) of Pol2C is 0. Subunits are listed above the bait protein when their interaction with the bait was increased upon α-amanitin treatment (log₂(H/M) versus 2C > 0), whereas subunits are listed below when their interaction with the bait protein was decreased upon α-amanitin treatment (log₂(H/M) versus 2C < 0). Interactions are considered significantly affected when log₂(H/M) versus 2C > 1 or log₂(H/M) versus 2C < −1 (equivalent to a change in value of 2-fold or greater).

Gene names	Accession numbers	No. of unique peptides	Sequence coverage	No. of peptides quantified	SILAC M/L ratio	log2(H/M) vs. 2C	(H/M) S.D.
			%				%
POLR2K	IPI00023975.1	3	53.4	3	56.2	0.51	3.4
POLR2L	IPI00003311.1	4	74.6	9	13.9	0.45	8.5
POLR2J	IPI00003310.2, IPI00873238.1, IPI00291359.3, IPI00884938.1, IPI00878433.1, IPI00553186.2, IPI00744926.1, IPI00472231.7, IPI00556199.1, IPI00016841.3, IPI00748167.1, IPI00879159.1, IPI00880135.1	4	57.5	21	21.2	0.35	15.5
POLR2B	IPI00027808.1, IPI00873948.2, IPI00894355.1, IPI00894141.1, IPI00418797.4, IPI00026445.3, IPI00184886.3, IPI00894524.1, IPI00894248.1	81	62.1	272	21.5	0.35	16.6
POLR2C	IPI00018288.1	17	85.8	73	12.4	0	24.1
POLR2A	IPI00031627.3, IPI00385524.1, IPI00419565.3, IPI00383337.1, IPI00784155.1	116	61.4	215	22.2	−0.97	36.1
POLR2D	IPI00007283.1	6	62	5	5.7	−1.14	26.4
POLR2H	IPI00003309.4, IPI00791019.1, IPI00790361.1, IPI00791273.1	8	58	12	29.9	−1.15	31.5
POLR2G	IPI00218895.6	11	74.4	14	11.2	−1.32	35.7
POLR2I	IPI00006113.1	7	78.4	9	20.1	−1.33	42.1
POLR2E	IPI00291093.3	10	58.1	23	27.6	−1.34	34.8