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pmid:26981347

The Escherichia coli transcriptome linked to growth fitness.

Bei-Wen Ying · Kazuma Yama · Kazuki Kitahara · Tetsuya Yomo

Genomics data · 2016 doi:10.1016/j.gdata.2015.11.011

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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2026-11-01T15:40:16Z
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title
The Escherichia coli transcriptome linked to growth fitness.
doi
10.1016/j.gdata.2015.11.011
pmid
26981347
authors array · 4 items
[0]
Bei-Wen Ying
[1]
Kazuma Yama
[2]
Kazuki Kitahara
[3]
Tetsuya Yomo
journal
Genomics data
year
2016
abstract
A series of Escherichia coli strains with varied genomic sequences were subjected to high-density microarray analyses to elucidate the fitness-correlated transcriptomes. Fitness, which is commonly evaluated by the growth rate during the exponential phase, is not only determined by the genome but is also linked to growth conditions, e.g., temperature. We previously reported genetic and environmental contributions to E. coli transcriptomes and evolutionary transcriptome changes in thermal adaptation. Here, we describe experimental details on how to prepare microarray samples that truly represent the growth fitness of the E. coli cells. A step-by-step record of sample preparation procedures that correspond to growing cells and transcriptome data sets that are deposited at the GEO database (GSE33212, GSE52770, GSE61739) are also provided for reference.
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Our studies critically consider the correlation between cell growth rate and the transcriptome.
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Our studies critically consider the correlation between cell growth rate and the transcriptome.
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The initial and final cell concentrations as well as the growth rates that correspond to the deposited GEO data sets are summarized in Table 1.
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The initial and final cell concentrations as well as the growth rates that correspond to the deposited GEO data sets are summarized in Table 1.
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Details on the cell samples used for the transcriptome analyses. The samples are indicated by the names of the E. coli strains used in the transcriptome studies and the number of replicas. The Temp., Initial conc., Final conc., and μ represent the temperatures for cell growth, the initial and final cell concentrations of the cultures, and the growth rate calculated using the initial and final cell concentrations as well as culture times, respectively. The Total cells indicate the number of cells used for the total RNA isolation, and the RNAs represent the quantity of total RNA purified from the cells. The cDNAs indicate the quantity of cDNAs that were reverse transcribed from every 10 μg of the total RNA.
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Precise measurement of the growth curve
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Table 1
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Details on the cell samples used for the transcriptome analyses. The samples are indicated by the names of the E. coli strains used in the transcriptome studies and the number of replicas. The Temp., Initial conc., Final conc., and μ represent the temperatures for cell growth, the initial and final cell concentrations of the cultures, and the growth rate calculated using the initial and final cell concentrations as well as culture times, respectively. The Total cells indicate the number of cells used for the total RNA isolation, and the RNAs represent the quantity of total RNA purified from the cells. The cDNAs indicate the quantity of cDNAs that were reverse transcribed from every 10 μg of the total RNA.
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Our studies critically consider the correlation between cell growth rate and the transcriptome.
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Complete file 
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