title: Agilent-033934 nONCOchip_2.0_26042011
status: Public on Jan 23 2015
contact.city: Leipzig
contact.first: Kristin
contact.last: Reiche
contact.email: kristin.reiche@izi.fraunhofer.de
contact.address: Perlickstr. 1
contact.department: Diagnostics
contact.country: Germany
contact.institute: Fraunhofer Institute for Cell Therapy and Immunology
organism: Homo sapiens
description: nONCOchip_2.0 design containing all custom probes, Agilent lincRNA probes, and Agilent mRNA probes (design id 026652).
  
  Arrays of this design have barcodes that begin with 16033934 or 2533934.
  
  The nONCOchip 2.0, a custom expression microarray, allows to facilitate the analysis of expression changes of disease-associated long non-coding RNAs in parallel with protein-coding genes (human genome version GRCh37/hg19). It comprises 913.413 probes of 60 base pairs each. In overall, 65% of probes correspond to long non-coding RNAs, while the remaining probes correspond to protein-coding mRNAs (20%) and regions antisense to 5’ or 3’ UTRs (11%). The nONCOchip 2.0 contains more than 160,000 probes (18%) for non-coding RNAs that are not available on any other commercial microarray platform. These probes represent RNAs that have been found to be controlled by major cancer-related pathways (controlled by oncogene Stat3, the tumor suppressor protein TP53 or by cyclins) and have been detected by transcriptome-wide expression variation studies utilizing Affymetrix Human Tiling Arrays (PMID 24594072). Further, the nONCOchip 2.0 covers a comprehensive set of known long non-coding RNAs retrieved from public databases as well as genomic regions with conserved secondary structure (identified by RNAz (PMID 15665081) or Evofold (PMID:16628248)).
  
  Orientation:
  Features are 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/