Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

BMC Genomics

Table 1 Results of cDNA-AFLP screens from ten recent publications.

RE1	RE2	PC	TDFs	Mean TDF	Corr. TDF	Reference
BstYI	MseI	60	4000	66.67	63	[29]
BstYI	MseI	64	3793	59.27	213	[30]
BstYI	MseI	128	10440	81.56	223	[31]
BstYI	MseI	128	7000	54.69	1196	[32]
BstYI	MseI	256	5900	23.05	378	[33]
EcoRI	MseI	64	3220	50.31	34	[34]
EcoRI	MseI	128	2269	17.73	25	[35]
EcoRI	MseI	256	12500	48.83	525	[36]
HindIII	MseI	32	4320	135.00	26	[37]
PstI	MseI	80	1200	15.00	46	[38]
	*Average*	119.6	5464.2	55.2	272.9
	*Median*	104.0	4160.0	52.5	138.0

TDFs are the number of transcript-derived fragments produced in each screen, while PC indicates the number of primer combinations tested in each study. Mean TDF indicates the average numbers of fragments generated per primer combination, while Corr TDF identifies the number of transcript-derived fragments that were found to be correlated to the trait under investigation. Restriction enzymes (RE) listed in column RE1 are characterized by recognition sites of 6 bp, while RE2 (here: MseI) is a 4 bp-cutter.

ISSN: 1471-2164