title: CUST-40K-Staphylococcus_epidermidis_RP62A
status: Public on Feb 28 2012
contact.city: Houston
contact.first: Mohan
contact.last: Pammi Venkatesh
contact.email: mohanv@bcm.edu
contact.state: TX
contact.address: One Baylor Plaza
contact.department: Pediatrics
contact.country: USA
contact.institute: Baylor College of Medicine
organism: Staphylococcus epidermidis RP62A
description: in situ synthesized oligonucleotide microarray
  Custom 40K Staphylococcus epidermidis RP62A MYcroarrays and each slide has one array composed of 40,960 spots
manufacture_protocol: In situ synthesized oligonucleotide microarrays were manufactured by MYcroarray and probe sequence designed using a proprietary version of OligoArray 2.0 (25). Arrays were synthesized on slide-sized glass substrates and each slide had one array composed of 40,962 spots, of which 33,715 spots contain 45mer probes for S. epidermidis genes, 525 empty features without a probe and 720 features with MYcroarray quality control probes. In addition, there are 6000 probes for randomly selected Candida genes to assess potential cross hybridization with S. epidermidis genes. There were up to 3 probes per gene and 5 identical replicates of each S. epidermidis probe. Multiple probes per gene format was chosen to account for the genetic variability between S. epidermidis 1457 strain used in our experiment compared to strain RP62A used in the microarray probe design. Also, to avoid theoretical cross contamination, S. epidermidis probes were blasted against C. albicans genome sequence (http://www.candidagenome.org) and S. epidermidis probes with potential match with C. albicans sequences were removed from the array design. Separately, RNA from pure C. albicans cultures were also hybridized to the arrays and cross-hybridizing probes were removed from data analysis.