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| Status |
Public on Oct 18, 2020 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Pseudomonas aeruginosa PAO1 Transcriptomes under AgNP and AgNR exposure |
| Organism |
Pseudomonas aeruginosa PAO1 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of Pseudomonas aeruginosa PAO1 in response to 0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, 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 Pseudomonas aeruginosa PAO1 in response to 0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, using Illumina HiSeq 2500
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| Contributor(s) |
Lu J, Guo J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Oct 18, 2019 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Jianhua Guo |
| E-mail(s) |
[email protected]
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| Organization name |
University of Queensland
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| Department |
Australian Centre for Water and Environmental Biotechnology
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| Street address |
Research Road, Level 4 Gehrmann Building
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| City |
Brisbane |
| ZIP/Postal code |
4072 |
| Country |
Australia |
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| Platforms (1) |
| GPL18782 |
Illumina HiSeq 2500 (Pseudomonas aeruginosa PAO1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA579069 |
| SRA |
SRP226701 |
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