Capture_2 using custom Mycroarray Capture Beads
A total of four regions on a 0.5 454 PTP plate were used to generate sequence capture data for this pilot experiment.  This means, 1/8 of a plate was used to sequence the captured products.  Capture 2 was composed of a mixture of Maxxa (MID1) and TX2094 (MID2) in 75:25 molar amounts prior to a common emPCR pool to prepare a single 'library' for sequencing.  The fragments of both libraries were independently captured using a custom Mycroarray Capture Beads containing DNA probes targeting 534 genes. The samples were independently captured on Mycroarray beads containing probes targeting 534 genes of the cotton exome.  The capture followed the recommended protocols from Mycroarray.  The samples were amplified after capture using the adapter sequences (LM-PCR).  The number of PCR cycles for LM-PCR was empirically determined using a test PCR sample (30 ul) and evaluation of amplificed products of every 5-cycle increment on a Lonza gel.