Table S2. Overview of results from the Cufflinks transcript assembly process.

Cufflinks assembles short reads aligned to a genome into a set of transcript fragments (‘transfrags’ or ‘transcripts’ or ‘txpts’, below), grouped by locus (‘gene’).

Tissue	Genes*	Multi-exon	Txpts/gene †	Transfrags	Single exon	Multiexon	Exons/txpt ‡
Adrenal	307,088	23,135	2.0	357,774	311,766	46,008	5.6
Adipose	134,348	21,793	1.5	158,142	126,207	31,935	6
Brain	239,971	24,435	1.8	218,818	238,497	43,321	6
Breast	191,620	23,553	1.6	222,525	185,869	36,656	5.5
Colon	116,723	23,503	1.3	133,953	103,071	30,882	5.1
Heart	149,951	21,537	1.5	177,059	144,829	32,230	6.5
Kidney	171,862	24,000	1.5	197,742	162,910	34,832	5.4
Liver	95,495	21,228	1.3	110,116	82,732	27,384	5
Lung	172,439	25,176	1.4	194,640	159,123	35,517	4.9
Lymph	188,709	23,766	1.5	216,692	179,938	36,754	4.9
Ovary	210,035	22,949	1.8	252,081	210,391	41,690	6.5
Prostate	161,526	24,584	1.4	186,159	150,732	35,427	5.5
Skel_muscle	95,684	19,695	1.2	105,209	82,359	22,850	4.7
Testes	220,459	29,546	1.6	259,043	212,894	46,169	5.9
Thyroid	187,169	23,357	1.8	224,647	184,751	39,896	6.3
White_blood	98,731	19,943	1.3	113,656	88,538	25,118	5.5

*Genes containing multi-exon transcripts.

^†Averaged over multi-exon genes.

^‡Averaged over multi-exon transcripts.