How to find sequencing data of a specific drosophila strain
As described in File S1 of Gutzwiller et al (2015) the relationship between the sub-strain of the ISO1 reference strain used by BDGP for the original Drosophila genome proejct, and the sub-strain in the Bloomington Drosophila Stock Center is complicated: 


  "We investigated the cause of the discrepancy of Wolbachia sequences in the Berkeley Drosophila Genome Project (BDGP) and Bloomington Drosophila Stock Center (BDSC) ISO1 genomic data by first establishing the provenance of these lineages. As documented in the BDSC database, the BDSC ISO1 sub-strain was donated directly to the stock center by Jim Kenni- son in 1994. The ISO1 sub-strain used by the BDGP was obtained from Gerry Rubin’s lab in the late 1990’s (Roger Hoskins, personal communication). The Rubin lab ISO1 sub-strain was obtained in the mid-1990s from Jim Kennison via at least one intermediate lab (Todd Laverty, personal communication). Thus, in contrast to naive assumptions, the ISO1 sub-strain at the Bloomington Drosophila Stock Center is neither a direct descendant nor progenitor of the ISO1 sub-strain used in the D. melanogaster genome project, and these two sub-strains have had independent trajectories since at least 1994."


The PacBio dataset you refer to was generated using the BDGP sub-strain. The Illumina data you refer to was generated using the BDSC sub-strain and is available here: https://www.ncbi.nlm.nih.gov/sra/ERX645969[accn]