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| Status |
Public on Jan 12, 2021 |
| Title |
Landscape of transcriptional and translational changes over 22 years of bacterial adaptation |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We use RNA-seq and Ribo-seq to analyze expression changes in the Long Term Evolution Experiment. By comparing expression levels between the ancestral strains and each of the evolved lines, we find that expression changes are largely parallel after 22 years of evolution, that these changes occur in specific pathways, and that known mutations may be responsible for some of the observed expression changes.
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| Overall design |
2 biological replicates each of RNA-seq and Ribo-seq of 13 E. coli cell lines. AraM and AraP refer to the 6 evolved lines of the ancestral REL606 and REL607 strains, respectively. Each file contains the data for the indicated biological replicate (rep1 or rep2), the indicated sequencing method (RNA-seq or ribo-seq), and the indicated cell lines (Ara-1-6 or Ara+1-6 and the corresponding ancestor). Code for processing the data can be found at https://github.com/shahlab/LTEE-gene-expression.
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| Contributor(s) |
Favate J, Liang S, Yadavali S, Shah P |
| Citation(s) |
36214449 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R35 GM124976 |
Dynamics and evolution of translational regulation |
RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY |
Premal R Shah |
| R01 DK056645 |
The LIN28b-Let7-IMP1 axis in colonic epithelial biology |
Trustees of Columbia University in the City of New York |
Anil K Rustgi |
| R01 DK109714 |
Homeostatic Responses to Amino Acid Insufficiency |
RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY |
Tracy G. Anthony |
| R01 DK124369 |
Defining post-transcriptional regulons in intestinal epithelial regeneration |
CHILDREN'S HOSPITAL OF PHILADELPHIA |
Kathryn Elizabeth Hamilton |
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| |
| Submission date |
Jan 05, 2021 |
| Last update date |
Nov 30, 2022 |
| Contact name |
Premal Shah |
| Organization name |
Rutgers University
|
| Department |
Genetics
|
| Street address |
145 Bevier Rd
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
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| Platforms (1) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA689830 |
| SRA |
SRP300526 |
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