Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and artificial sweeteners-stressed Acinetobacter baylyi ADP1 and pWH1266 plasmid Transcriptomes

ABSTRACT: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type Acinetobacter baylyi ADP1 and Pwh1266 plasmid, and their mRNA response under the exposure of four artificial sweeteners, including saccharin, sucralose, aspartame, and acesulfame potassium. 3 mg/L of each sweetener was used to treat the mixture of bacteria cell and plasmid. The group without dosing any artificial sweeteners was the control group. Each sample was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these four artificial sweeteners on the transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. 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 Acinetobacter baylyi ADP1 reference genome (NC_005966) 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 culture. 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.

ORGANISM(S): Acinetobacter baylyi ADP1

PROVIDER: GSE141954 | GEO | 2021/09/20

REPOSITORIES: GEO