transcriptomics



High throughput sequencing of Brassica transcripts

Current technologies for establishing transcriptome composition are based on high throughput sequence analysis of transcripts, using approaches such as RNA-seq. As of Jan 2015, there are 889 Sequence Read Archive objects in the NCBI database. This relates to 50 studies.



Micro-array platforms

A summary of available Brassica micro-arrays and links to datasets have appeared here as they became available. There has also been successful use of cross-species hybridisation link to the Affymetrix Arabidopsis GeneChip (R).
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.nbi.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.


This Page Was Last Edited: 08-Jan-2015