barseed

This database contains the expression data and co-expression patterns of identified modules from the study discussed in manuscript "The dynamics of transcript abundance during cellularisation of developing barley endosperm."

Endosperm from developing barley grain from 3 DAP to 8 DAP were collected and subject to transcriptome profiling using a custom microarray representing 42,908 barley sequences. A gene co-expression network was constructed based on 5,925 differentially expressed probes (between any two time points) and 47 co-expression modules were identified as a result.

Probe expression profiles across 6 time points from each module can visualized and each probe can be interrogated individually by mousing over or clicking on its expression profile. The link will lead to a new page showing details such as probe id, probe sequence, raw and normalized expression values, best BLAST hit to the barley predicted genes (MLOCs) with corresponding Affymatrix probes, contig sequence and homologues to other model plant species.

The list of cell wall related probes collected from CAZy website and the Cell Wall Navigator were also listed separately for interrogation. You can now start by clicking "List Cluster sets" or "List cell wall probes" on the navigation panel on the left of the page.

Alternatively, you can search for an Agilent Barley microarray probe ID, or a barley predicted transcript (MLOC ID) as well as a Affymetrix Barley 1 GeneChip ID if you want to interrogate a gene of interest on the homepage. It will leads you to the detailed information about this gene and corresponding clusters through Agilent probe ID or MLOCs.

For more barley microarray expression data on different tissues, you can also visit our morexGenes website and also the Barley eFP Browser

Search for an Agilent Barley microarray probe ID

A custom microarray SCRI_Hv35_44k_v2, based on the HarvEST 35 EST assembly (Agilent design 023660; ArrayExpress accession A-MEXP-2404). More details of the assembly and how it as made can be found at the HarvEST site.

e.g. CUST_130_PI415269222

  

Search for a barley predicted transcript

The set of predicted transcripts from the IBGSC (abstract). MLOC 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.

e.g. MLOC_20815.1

  

Search for a Affymetrix Barley 1 GeneChip ID

Based on the HarvEST 21 EST Assembly (abstract). More details of the assembly and how it as made can be found at the HarvEST site.

e.g. ABC19065