Illumina MiSeq Resequencing of WT and Acid Tolerant Fibrobacter succinogenes S85
Illumina PE TruSeq libraries were prepared as described in the manufactures methods (Part# 15005180 RevA) following the low throughput protocol.  In short, 3 ug of DNA was sheared to a size between ~200 bp and 1000bp by nebulization (nitrogen) for 1 min at 30psi.  The sheared DNA was purified on a Qiagen Qiaquick Spin column (Qiagen).  The sheared material was accessed for quantity with a Qubit broad range double stranded DNA assay (Life Technologies) and quality by visualization on an Agilent Bioanalyzer DNA 7500 chip (Agilent).  One microgram of sheared DNA was used for library preparation following the manufactures method.   Steps included end repair followed by an AMPure XP bead clean up, adenylation of 3’ ends and adapter ligation followed by a second AMPure XP bead clean up, purification of the library by gel selection, DNA enrichment with 10 cycles of amplificaiton and a final AMPure XP bead clean up.  Libraries were validated by Qubit (Life Technologies) and visualized by Agilent Bioanalyzer for appearance and size determination.  Samples were normalized using the Illumina’s Library dilution calculator to a 10nM stock.  Sequencing was completed on a Illumina MiSeq with a v2 500 cycle MiSeq kit sequencing 2 x 251 with 8bp for the index.