title: Mouse MuscleArray 1.0
status: Public on Sep 21 2005
contact.city: Padova
contact.first: Paolo
contact.last: Laveder
contact.email: laveder@cribi.unipd.it
contact.address: via U.Bassi 58/B
contact.department: Department of Biology
contact.country: Italy
contact.web_link: http://muscle.cribi.unipd.it/microarrays/index.html
contact.institute: CRIBI Biotechnology Center
contact.phone: 0039 0498276221
organism: Mus musculus
description: 2,061 muscle-specific cDNA probes (300-600 bp), restricted to the 3'-end of each mRNA, were spotted in quadruplicates.
  
  MICROARRAY FABRICATION:
  The cDNA inserts were cloned in the plasmid vector pZErO-1 (Invitrogen) and amplified by PCR with universal primers (A: 5’-TCCGGCTCGTATGTTGTGTGG-3’, B: 5’-GTTGTAAAACGACGGCCAGTG-3’). The quality of each amplicon was monitored on agarose gels: cDNA probes showing more than a single size product, described by a ‘WARNING’ message, were excluded from subsequent microarray analyses. PCR reactions were transferred to 96-well MicroAmp Optical plates (PerkinElmer) and precipitated with ethanol and salt, following a clean-up protocol developed at the Stanford University. The microarray facility at CRIBI managed microarray printing and post-processing (http://microcribi.cribi.unipd.it/). cDNA probes were spotted on glass slides across an area of 18 x 18 mm, using a Genpak Array 21 robotic system (Genetix, Hampshire, United Kingdom) equipped with 16 Stealth Micro Spotting Pins SMP 3B (ArrayIt): spots have an average diameter of 120 µm, the distance between two spots is 180 µm, each cDNA probe is spotted in four replicates.
  
  GENE ANNOTATION:
  The cDNA sequences were aligned on the mouse genome (NCBI Build 32) at the UCSC Genome Browser, using the BLAT software. Known genes are described as LocusLink entry; cDNAs of uncertain origin are marked as ‘SIMILAR TO’ or ‘UNKNOWN’, depending if they have similarity or not to other expressed sequences in GenBank. We realized that 8.4% of cDNA probes are possibly redundant, due to multiple isoforms, alternative mRNA terminations, or to cDNA covering different sequences of the same transcript.