I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc. I have tried GEO but it only gives a list and one should read all pages and samples one by one to see which conditions were used.
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1$\begingroup$ What do you mean with "different condition"? GEO is a database which holds gene expression data, so it is not the place to look for whole genomes. If you look for gene expression data instead, please adapt your question. Information about different complete E.coli genomes can be found here $\endgroup$– Chris ♦Commented Apr 2, 2015 at 9:58
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$\begingroup$ @Chris I modified my question $\endgroup$– LearnerCommented Apr 2, 2015 at 10:32
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$\begingroup$ Are you looking for something that would give you a list of what genes are expressed under specific conditions? $\endgroup$– Nandor PokaCommented Apr 2, 2015 at 10:37
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$\begingroup$ you can run an automated GEO query and fetch GEO accession numbers for the ones that match your keywords. $\endgroup$– WYSIWYGCommented Apr 2, 2015 at 12:41
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$\begingroup$ If you are interested in sequencing data then search NCBI-SRA $\endgroup$– WYSIWYGCommented Apr 2, 2015 at 12:42
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There are some databases in which you can search for E.coli gene expression data:
- GenExpDB: E. coli Gene Expression Database
- Many Microbe Microarrays Database (M3D): A resource of microbial gene expression data
- Stanford MicroArray Database (use the search tool to find relevant organisms)
- Colombos (COLlection Of Microarrays for Bacterial OrganismS)
- ArrayExpress
To find out about the purpose and the conditions of the experiments behind this data sets you will have to read the respective publications.
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$\begingroup$ can you please post some example papers done for E coli gene expression data if you are aware of any $\endgroup$– LearnerCommented Apr 2, 2015 at 14:47
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2$\begingroup$ @Nemo lmgtfy.com/?q=e.coli+gene+expression+studies $\endgroup$ Commented Apr 2, 2015 at 15:28