- morexGenes - Barley RNA-seq Database
This website provides access to the predicted genes from an assembly of whole-genome-shotgun sequence from barley (Morex). The genes were predicted from the mapping of RNA-seq data to the genomic assembly. Gene expression levels were also calculated from the RNA-seq data and are available in the form of FPKM values associated with the predicted genes.
You can access data directly by searching for a particular sequence ID or microarray probe ID (currently only available for the Morex 60K Agilent microarray chip, see below), or by BLASTing a sequence
against the genomic contigs, gene CDS or proteins on the BLAST page. If you don't have a DNA or protein sequence, you can use the keyword search
on the BLAST annotations of the genes, which are available for the Rice Pseudo-peptides v6
and the TAIR Arabidopsis thaliana Pseudo-peptides v10
Search for a sequence ID
The set of barley genomic contigs, predicted genes and transcripts from the IBGSC (abstract). Genomic contig IDs have the form contig_48487. Transcript IDs have the form MLOC_1.1, denoting transcript 1 from gene region MLOC_1. The set of transcripts also includes some full length cDNAs and are denoted by their NCBI nucleotide database accession ID e.g. AK375833. More information about the transcripts can be seen at morexGenes.
The morex 60K Agilent microarray
A custom-designed barley Agilent gene expression microarray (A-MEXP-2357; www.ebi.ac.uk/arrayexpress) has been developed at the James Hutton Institute. The microarray contains c. 61,000 60-mer probes derived from predicted transcripts of the barley reference sequence assembly (IBGSC, 2012) and full-length cDNAs. The array design is in 8x 60k format and is available to order from Agilent, please contact Pete Hedley for details (email@example.com
Search for a microarray probe ID
Barley Plant Material and RNA Preparation
In total, 8 barley tissues were prepared for generation of a reference set of RNA-seq data.
|Tissue abbreviation||Tissue description|
|EMB||4-day embryos dissected from germinating grains|
|ROO||Roots from the seedlings (10 cm shoot stage)|
|LEA||Shoots from the seedlings (10 cm shoot stage)|
|INF1||Young developing inflorescences (5mm)|
|INF2||Developing inflorescences (1-1.5 cm)|
|NOD||Developing tillers at six-leaf stage, 3rd internode|
|CAR5||Developing grain, bracts removed (5 DPA)|
|CAR15||Developing grain, bracts removed (15 DPA)|
Further details of the plant material and images of the selected tissues are available here.