transcriptomics

Determining sets of transcripts from the Brassica genomes

A summary of available Brassica micro-arrays and links to datasets will appear here as they become available. There has also been successful use of cross-species hybridisation link to the Affymetrix Arabidopsis GeneChip (R). Transcriptional data will also become available derived from massively parallel sequencing (e.g. Solexa).


Micro-array platforms

Platform Details Availability Related datasets
Affymetrix

GeneChip® Brassica Exon 1.0 ST Array, now available; outline information Jan 2010 pdf

 

Love et al. (2010) paper in PLoSONE

 2010 from NASC

readme.txt;

135k Unigene sequences

135k Exon sequences

Alignment to Arabidopsis

       
*Agilent 95k Paper in BMC Plant Biology (2009) pdf
download presentation pdf
Cogenics information link 		JIC / JCVI / Cogenics link  
       
Combimatrix NRC, Canada abstract at PAG XVI link  
       
Nimblegen link  B. rapa EST & microarray database (BrEMD) KBGP 24k array link  
       
cDNA NRC, Canada abstract at PAG XIV link  
*The Agilent Brassica array is now available from Cogenics. Cogenics have agreed to authorize access for everyone but their direct commercial competitors who provide microarray services. A document needs to be signed for use. The unigenes associated with the probes are the unigenes are already publicly available via the Brassica Genome Gateway (http://brassica.bbsrc.ac.uk/), where they have been annotated for the probe sequences, and are included in the B. rapa BAC annotations. The availability of the probe sets has yet to be clarified.

Transcriptomic datasets




This Page Was Last Edited: 15-Feb-2011