Difference between revisions of "List of useful Datasets"
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A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. | A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. | ||
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'''CREP Database''' (wang et al, 2010) [http://crep.ncpgr.cn Collections of Rice Expression Profiling] | '''CREP Database''' (wang et al, 2010) [http://crep.ncpgr.cn Collections of Rice Expression Profiling] | ||
Revision as of 17:15, 6 December 2010
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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)
-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
Rice Array Database (RAD) is a public resource for gene expression analysis in rice, the most important staple food over the world. Over 1,000 microarray slides were incorporated and several kinds of analysis tool are available in RAD.
GEO Gene Expression Omnibus (NCBI)
A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
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
