The short reads from the four libraries were assembled by SOAPdenovo 1.04 [ 36] with optimal assembly acquired with the key parameter K = 55.
The four libraries amount to 68,000 square feet of library space, the product of a bond measure that passed in 2000 at the height of the Internet bubble.
When all the unique, reliable, and significant signatures (≥4 TPM) from the four libraries were clustered, a total of 37,532 unique signatures were obtained.
The GA-enriched library was the best among the four libraries in terms of number of alleles, polymorphism, productivity, and information content.
The GA-enriched library was the best, whereas the AAC library was the worst among the four libraries in terms of perfect repeats, number of alleles, polymorphism, and informativeness.
Each of the four libraries were independently sequenced using high-throughput pyrosequencing [21].
We obtained ∼32 million 36-mer readseads for the four libraries, two biological replicates for each condition.
Ninety-six of the most intensely biotinylated, hexahistidine-positive clones from each of the four libraries were grown in 4 ml volumes and protein expression induced.
Equal amounts of cDNA from each sample were pooled to construct the four libraries using cDNAs from 2 and 24 hours infected minus non-infected insects and 2 and 24 hours non-infected minus infected insects.
The four libraries were sequenced unidirectionally in the reverse direction (B-adaptor) during two 454 Genome Sequencer FLX (GS-FLX, 454 Life Sciences (Roche), Branford, CT 06405 USA) runs.
In the present study, although excess human rRNA was removed before cDNA synthesis by column hybridization (see methods), for the four libraries residual rRNA still comprised 19.9+/−1.21% of the sequence data.
