What is on the Barley1 GeneChip?

In general, probe sets on the Barley1 GeneChip are composed of 11 pairs of 25-mer oligonucleotide derived principally from the last 600 bases of each exemplar consensus sequence or singleton sequences. The term "probe" refers to the fixed nucleic acid molecules used to interrogate the experimental samples, while "target" refers to the experimental sample (i.e., the labeled RNA). Each probe pair contains a perfect match oligonucleotide and a mismatch control containing a single substitution at the 13th base. Technical notes on GeneChip arrays and their operation can be found at the Affymetrix website. Oligonucleotide placement within each represented exemplar sequence can be viewed online from BarleyBase, or on Windows computers using HarvEST:Triticeae.  Annotation information for the Barley1 array is hosted on the NetAffx Analysis Center at Affymetrix (http://www.affymetrix.com/support/technical/byproduct.affx?product=barley1)

Search and Access Probe Sets on Barley1:

There are  five ways to access probe sets on Barley1 GeneChip.

• Search by Gene Expression Profiles:  Finding probe sets showing desired expression profile in absolute value and in variation using multiple filters. It can be conducted on a single experiment basis, or on cross-experiment basis.

• Browse by Probe Set List:  All microarray elements can be retrieved from the list of probe sets,

• Sequence Similarity-Based Search

  There are two  major options, either through courtesy of the PlantGDB or Gramene databases, or locally at BarleyBase.

  Option 1. Search for Barley1 GeneChip content with user's own sequences

  • BarleyBase BLAST page for Barley1 and Arabidopsis ATH1-121501 GeneChip Exemplar Sequences.
  • PlantGDB Dedicated BLAST page for Barley GeneChip Exemplar Sequences.
  • PlantGDB Dedicated VMATCH page to search against Barley1 GeneChip probes. This tool  match your sequences against Barley GeneChip probes. The result tells you if there is a match and where the match occurs. It is useful for biologists to find out if there are available oligo probes for their sequences.

  Option 2. Searches starting with Barley1 GeneChip exemplar sequences

  • Find microarray oligo probe (set) for a known Barley1 contig: 
    For  example: http://www.plantgdb.org/data.php?Seq_ID=Barley1_03970, which displays details of the exemplar sequence, its member ESTs and alignments, and its oligo probes..
  • NCBI BLAST Search against the comprehensive NCBI's GenBank with Barley1 GeneChip Exemplars.
  • Align Barley1 exemplar sequences with other cereal genes and genomes on the Gramene Rice Genome Browser (http://www.gramene.org/) for cross-species comparison.
• Input one Probe Set Name to align it with exemplar sequence, or retrieve expression of a list of Probe Sets.

 

• Keyword-Based Search.

   Construct complex search terms with keywords and Boolean operators to search against the exemplar sequence annotations.