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GenoBase: comprehensive resource database of Escherichia coli K-12.

Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, Conway T, Gribskov M, Kihara D, Rudd KE, Tohsato Y, Wanner BL, Mori H - Nucleic Acids Res. (2014)

Bottom Line: Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes.Quality control is extremely important for evaluating results generated by these resources.Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.

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Genomic structure of target region of deletion collections. Two sets of deletion collections have been constructed using the same primer set. The deleted regions are the same between Keio and Barcode collections. FRT in the Keio and FRT1 of the Barcode collection are not site-specifically recombined by FLP recombinase.
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Figure 4: Genomic structure of target region of deletion collections. Two sets of deletion collections have been constructed using the same primer set. The deleted regions are the same between Keio and Barcode collections. FRT in the Keio and FRT1 of the Barcode collection are not site-specifically recombined by FLP recombinase.

Mentions: Our database is focused on information about our comprehensively constructed experimental resources (libraries of plasmid clones, deletion mutants, etc.) and HT experimental data from a large E. coli functional genomics project that far exceeds all other resources combined. All the information in GenoBase is publicly available. Current resources include: four types of annotated Open Reading Frame (ORF) plasmid clone libraries and two types of deletion collections. The plasmid clone libraries include: the ASKA ORFeome libraries with (A) and without (B) a C-terminal GFP fusion (9,25), Gateway entry clone library (C; (25)) and the latest TransBac library (H. Dose, unpublished) as shown in Figure 3. The single-gene deletion collections include: the Keio collection (A; (8)) and a recently constructed barcode deletion collection (B) as shown in Figure 4. The Barcode deletion collection, whose manuscript is now in preparation, was originally constructed for the systematic analysis of synthetic lethal/sickness genetic interaction to make double genes knockout by combining single-gene deletion from the Keio and the barcode collection by conjugation (26,27, R. Takeuchi, unpublished). We added a further valuable feature, 20-nt molecular barcode, which makes population analysis and multiplex parallel screening of mixed cultures feasible (Y. Otsuka et al., unpublished).


GenoBase: comprehensive resource database of Escherichia coli K-12.

Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, Conway T, Gribskov M, Kihara D, Rudd KE, Tohsato Y, Wanner BL, Mori H - Nucleic Acids Res. (2014)

Genomic structure of target region of deletion collections. Two sets of deletion collections have been constructed using the same primer set. The deleted regions are the same between Keio and Barcode collections. FRT in the Keio and FRT1 of the Barcode collection are not site-specifically recombined by FLP recombinase.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383962&req=5

Figure 4: Genomic structure of target region of deletion collections. Two sets of deletion collections have been constructed using the same primer set. The deleted regions are the same between Keio and Barcode collections. FRT in the Keio and FRT1 of the Barcode collection are not site-specifically recombined by FLP recombinase.
Mentions: Our database is focused on information about our comprehensively constructed experimental resources (libraries of plasmid clones, deletion mutants, etc.) and HT experimental data from a large E. coli functional genomics project that far exceeds all other resources combined. All the information in GenoBase is publicly available. Current resources include: four types of annotated Open Reading Frame (ORF) plasmid clone libraries and two types of deletion collections. The plasmid clone libraries include: the ASKA ORFeome libraries with (A) and without (B) a C-terminal GFP fusion (9,25), Gateway entry clone library (C; (25)) and the latest TransBac library (H. Dose, unpublished) as shown in Figure 3. The single-gene deletion collections include: the Keio collection (A; (8)) and a recently constructed barcode deletion collection (B) as shown in Figure 4. The Barcode deletion collection, whose manuscript is now in preparation, was originally constructed for the systematic analysis of synthetic lethal/sickness genetic interaction to make double genes knockout by combining single-gene deletion from the Keio and the barcode collection by conjugation (26,27, R. Takeuchi, unpublished). We added a further valuable feature, 20-nt molecular barcode, which makes population analysis and multiplex parallel screening of mixed cultures feasible (Y. Otsuka et al., unpublished).

Bottom Line: Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes.Quality control is extremely important for evaluating results generated by these resources.Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.

Show MeSH
Related in: MedlinePlus