title: Agilent-025771 UCSF Multi-species custom array miRNA-v3.5-8x15k
status: Public on Dec 19 2011
contact.city: San Francisco
contact.first: Andrea
contact.middle: J
contact.last: Barczak
contact.state: CA
contact.address: 1550 4th St Rock Hall 545
contact.country: USA
contact.institute: UCSF Sandler Center Functional Genomics Core Facility
organism: Caenorhabditis elegans
  Drosophila melanogaster
  Danio rerio
  Gallus gallus
  Homo sapiens
  Mus musculus
  Rattus norvegicus
description: miRNA microarray probe design, v3.5 (10/15/09)
  Mirbase 14, hsa, mmu, dre, gga, rno, dme, cel
  
  Total unique probe sequences:
  2405(miR)+14(siRNA)+24(snRNA)+16(snoRNA)+3(tRNA)+30(spike-in)+30(mRNA)+192 = 2714
  
  For the 2405 miRNA probes, 6 replicates were generated
  For the 117 control probes, 5 replicates were generated
  For the 192 mismatch probes, 1 replicate
  Total UCSF probes: 15207
  Agilent Controls: 536
  Total probes on array: 15743  + 1 empty = 15744
  
  NOTE: Platform ID column lists probe IDs from array design v3.5.  Core Annotation file (see design_cross_ref-5.txt below) shows relationships among the probeIDs in array designs v3.4 (Agilent-023723), v3.5 (Agilent-025771), and v3.6 (Agilent-031052).
  
  Arrays of this design have barcodes that begin with 16025771 or 2525771.
  
  Orientation:
  Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
  
  The ID column represents the Agilent Feature Extraction feature number.
  
  Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
  
  To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
manufacture_protocol: see manufacturer's web site at http://www.agilent.com/