Table 1.

Statistics for ESTs generated for all SSH libraries¹

Library Name	HK_F	HK_R6	SM_F	L_F	L_R
Tissue	Head Kidney	Head Kidney	Skeletal Muscle	Liver	Liver
Direction2	forward	reverse	forward	forward	reverse
CGP ID3	sb_gmnlkfta	sb_gmnlkrta	sb_gmnlmfta	sb_gmnllfta	sb_gmnllrta
# of ESTs	1451	93	1419	1524	1586
Average EST length4	297 bp	400 bp	340 bp	241 bp	227 bp
# of contigs5	212	8	159	200	178
# of singletons	746	35	483	612	668
# of non- redundant ESTs7	958	43	642	812	846
% redundancy8	33.9%	53.7%	54.7%	46.7%	46.6%

¹Agarose gel electrophoresis of the muscle reverse library revealed the presence of 5 clear bands, which indicated a low-complexity library. Therefore, sequencing of this library was not attempted.

²The forward SSH libraries were constructed to be enriched for genes that were up-regulated by heat-shock, and the reverse SSH libraries were constructed to be enriched for genes that were down-regulated by heat-shock.

³The identifiers (ID) or names of the SSH libraries in the CGP EST database: http://www.codgene.ca.

⁴The ESTs were trimmed with Phred [62,63] with the trim_alt and trim_cutoff fixed at 0.06, followed by the removal of known contaminant sequences and short sequences (< 75 bp), and the average EST length was calculated based on edited sequences.

⁵Sequences generated were then clustered using Paracel Transcript Assembler (PTA), with the cluster threshold set at 100 for relatively stringent clustering.

⁶The 4 largest contigs in this library (Additional file 2, Table S2A) were annotated as haemoglobins and contained 45 sequences, which represented almost 50% of the good sequences obtained for it. Thus, this library was deemed low-complexity and not sequenced further.

⁷The number of non-redundant ESTs is the sum of the number of contigs plus the number of singletons.

⁸Percent redundancy is the proportion of redundant ESTs in each library, calculated as [1 - (Number of non-redundant ESTs/total number of ESTs)] multiplied by 100.