title: CapitalBio human/mouse/rat non-coding RNA microarray
status: Public on Sep 21 2008
contact.city: Guangzhou
contact.first: Jian-Rong
contact.last: Yang
contact.address: No. 74, Zhongshan 2nd Road
contact.country: China
contact.institute: Sun Yat-sen University
organism: Homo sapiens
  Mus musculus
  Rattus norvegicus
manufacture_protocol: Mature miRNA sequences were downloaded from the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 7.0, accessed June. 2005). We collected 347 human/mouse/rat mature miRNA sequences in the microarray. All miRNA probe sequences were designed to be complementary to the full-length mature miRNA. 122 predicted miRNA sequences (i.e., Nature PREDICTED_MIR* array features in the Description column) from a published reference (Xie et al., Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 2005 Mar 17;434(7031):338-45) were also included. The miRNAs described as "Cell_predict*" probes were designed after the predicted human miRNAs from this paper: Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RHA, Cuppen E: Phylogenetic shadowing and computational identification of human microrna genes. Cell 2005, 120:21-24. Sequences of human tRNA and rRNA shorter than 200nt were downloaded from Rfam. And as for the 281 snoRNA and other non snRNA shorter than 200nt, they were downloaded from snoRNA-LBME-db (http://www-snorna.biotoul.fr/index.php) and NONCODE (http://noncode.bioinfo.org.cn/) respectively. After removing the redundancy sequences, we designed 2115 probes complementary to these non-coding RNAs.
  In addition, we designed 8 short oligos (i.e., Y2, Y3, Zip*) possessing no homology with all existed RNA sequence and produced their corresponding synthetic miRNAs by in vitro transcription using Ambion's miRNA Probe Construction kit (Cat#. 1550). We spike various amounts of synthetic miRNAs into the interrogated RNA samples.
  To facilitate probe immobilization on aldehyde modified glass slides, the probe sequence were concatenated up to 40 nt and modified with 5'-amino-modifier C6. Oligonucleotide probes were synthesized at MWG Biotech. Company and dissolved in EasyArray(TM) spotting solution (CapitalBio Corp.) at 40 uM concentration. Each probe was printed in triplicate using a SmartArrayTM microarrayer (CapitalBio Corp.); the data table below corresponds to the condensed representation of the array.