List of useful Datasets

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Genevestigator

Organisms: High quality sources only:

Arabidopsis thaliana source expts:

• AG 8K array, 90 expts

NASC (72), GEO (18)

• ATH1: 22K array: 5760 expts

-Gruissem lab (18), NSAC (326), FGCZ (55), GEO (2731), ArrayExpress (1679), AtGenExpress (876), TAIR (38), other (37)

Oryza sativa source expts:

• Os_51K Rice Genome Array 51K: 162 expts:

GEO (151), PlexDB (11)

Rice Gene Expression Atlas (Wang et al, 2010)

• Affymetrics GeneChip® Rice Genome Array

-contains 57,381 probe sets in total, of which 1347 represent 1260 transcripts of an indica variety and 54 168 represent 48 564 transcripts of a japonica variety.

• 31 tissues/organs from throughout the plant life cycle,from two indica varieties; Zhenshan 97 and Minghui 63.
• 8 (callus) samples spanning the tissue culture process of genetic transformation were also included,
• Total number of tissues were 39- this is actually only 15 different tissues/organs, but some were taken at different developmental stages ( ).

-germinating seed

-plumule (2)

-radicle (2)

-seedling (5)

-leaf sheath (2)

-stem (2)

-leaf (4)

-palea + lemma

-stamen

-spikelet

-endosperm (3)

-panicle (5)

-root

-shoot

-Callus (8)

Data was deposited in the database CREP Collections of Rice Expression Profiling.

-It can be searched by querying single gene or multiple genes using gene sequences, gene names, or the probe identifications, for items like quantified expression values, the co-expressed genes, the tissues and varieties in which they are expressed.

Other sources of micorarray data:

UC Davis Ricearray.org

GEO Gene Expression Omnibus

CREP Database (wang et al, 2010) Collections of Rice Expression Profiling

PlexDB Plant Expression Database

EBI ArrayExpress Archive- a database of functional genomics experiments including gene expression Gene Expression Atlas