Skip to main content

Table 1 Statistics for ESTs generated for all SSH libraries1

From: Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques

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%
  1. 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.
  2. 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.
  3. 3The identifiers (ID) or names of the SSH libraries in the CGP EST database:
  4. 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.
  5. 5Sequences generated were then clustered using Paracel Transcript Assembler (PTA), with the cluster threshold set at 100 for relatively stringent clustering.
  6. 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.
  7. 7The number of non-redundant ESTs is the sum of the number of contigs plus the number of singletons.
  8. 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.