title: [CINT06a520380F] Affymetrix Ciona intestinalis custom-designed array
status: Public on Jun 05 2012
contact.city: Tucson
contact.first: Bradley
contact.middle: J
contact.last: Davidson
contact.email: bjd18@email.arizona.edu
contact.state: AZ
contact.address: PO Box 245217
contact.department: Molecular Cardiovascular Research Program
contact.country: USA
contact.web_link: http://www.mcrp.med.arizona.edu/html/braddavidson
contact.institute: University of Arizona
contact.phone: 520 626-8113
organism: Ciona intestinalis
description: Probe identifiers:
  
  There are a few different types of probe identifiers, including:
  
  * MKG.<number>.<number>_s<OptionalNumber>_at
  * Fis_ciad<number>_at
  * TGxxxxx_at
  * Gastxxx_at
  * Zellerxxx_at
  
  A probe identifier in the format MKG.7.115_s_at indicates that this probe targets the gene model KYOTOGRAIL2005.7.115 described in the http://aniseed.cnrs.fr database. The suffixes s0, s1, s2, etc. signify different "supplemental" gene models for the same locus.
  
  The Aniseed transcript model pages for these models are located at URLs such as: http://www.aniseed.cnrs.fr/molecule-gene.php?name=KYOTOGRAIL2005.7.115.1
  
  The Fis and TG probe identifiers refer to additional gene models based on EST data that were not covered by the KyotoGrail predictions. A probe identifier like Fis_ciad008l03 is based on a full-insert sequence. These have been submitted to GenBank and can be found in the GenBank EST section, e.g., http://www.ncbi.nlm.nih.gov/nucest?term=ciad008l03 .
  
  The GastmiR and ZellerMiR identifiers are probe sets against Ciona microRNAs models.  The models were generated by the labs of Terry Gaasterland (UCSD) and Robert Zeller (SDSU), respectively.
  
  Gene identifiers:
  
  The Platform table includes a "jgi1_GeneID" column with JGI1 gene model identifiers. JGI1 identifiers have the format ci0100<number>.
  
  Further information on these JGI1 gene models can be found at URLs such as:
  http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=ciona4&id=142570
  http://ghost.zool.kyoto-u.ac.jp/cgi-bin/gb2/gbrowse/kh/?name=mRNA%3Aci0100142570;dbid=clone%3Adatabase
  http://www.aniseed.cnrs.fr/molecule-gene.php?name=ci0100142570
  
  This array is also described in ArrayExpress (http://www.ebi.ac.uk/arrayexpress/arrays/A-AFFY-106).
  
  The oligonucleotide sequences are available in the supplementary file GPL15657_probe.fa.gz.
manufacture_protocol: See manufacturer's website (www.affymetrix.com).