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| Status |
Public on Dec 20, 2018 |
| Title |
Pseudogene repair driven by selection pressure applied in experimental evolution |
| Organism |
Escherichia coli K-12 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We performed evolution of ∆menF∆entC strain of Escherichia coli K12 MG1655 to study how the system adapt to the loss of siderophore biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring.
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| Overall design |
Growth of E. coli with various supplements was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.
ALE is the acronym for adaptive laboratory evolution. ALE_39.91, ALE_29.82 and ALE_30.83 are the independent biological replicates of ∆menF∆entC which are evolved in our laboratory to study how the strains adapt to the loss of the menF and entC genes. Similarly, ALE_36.86, ALE_37.25 and ALE_38.28 are the independent biological replicates of ∆menF∆entC∆ubiC which are evolved in our laboratory to study how the strains adapt to the loss of the menF, entC and ubiC genes.
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| Contributor(s) |
Anand A, Sastry AV |
| Citation(s) |
30692668 |
| |
| Submission date |
Nov 20, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Amitesh Anand |
| E-mail(s) |
amiteshanand@eng.ucsd.edu
|
| Phone |
858-246-1625
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| Organization name |
UCSD
|
| Department |
Bioengineering
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| Lab |
Systems Biology Research Group
|
| Street address |
9500 Gilman Drive
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL24377 |
Illumina HiSeq 4000 (Escherichia coli K-12) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA506264 |
| SRA |
SRP169967 |
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