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| Status |
Public on Dec 01, 2018 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and mutant E. coli K-12 MG1655 Transcriptomes |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 MG1655 and triclosan induced E. coli mutants in response to 0.2 mg/L triclosan for 8 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
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| Overall design |
Bacterial mRNA profiles of wild-type E. coli K-12 MG1655 and triclosan induced E. coli mutants in response to 0.2 mg/L triclosan for 8 h, in triplicate, using Illumina HiSeq 2500
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| Contributor(s) |
Lu J, Jin M, Guo J, Mao L |
| Citation(s) |
29902774 |
| |
| Submission date |
Nov 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianhua Guo |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Queensland
|
| Department |
Australian Centre for Water and Environmental Biotechnology
|
| Street address |
Research Road, Level 4 Gehrmann Building
|
| City |
Brisbane |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
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| Platforms (1) |
| GPL18956 |
Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA418956 |
| SRA |
SRP125211 |
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