title: Sigma1278b genome sequence by short reads
design: Samples for Solexa sequencing were purified using the protocols outlined in Illumina Genomic DNA sample prep kit.  5 ug of genomic DNA was fragmented by sonication and the ends were repaired by T4 polynucleotide kinase, T4 DNA polymerase, and Klenow.  Next, an A base was added to the 3' end of the blunt phosphorylated DNA fragments using Klenow fragment lacking exonuclease activity.  Solexa adapters were ligated to the ends of the DNA fragments.  The products from the ligation reaction were separated by gel electrophoresis, and ligation products corresponding to 150BP were purified using a Qiagen gel extraction kit.  We enriched for fragments containing both ligated primers by performing 18 cycles of PCR.  The PCR library was validated by electrophoresis and the concentration of DNA was determined by nanodrop.  Three lanes of cluster generations were performed on an Illumina cluster station using 2pM sequencing libraries for each  lane.