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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: http://www.codgene.ca.
  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.