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Sample GSM4135986 Query DataSets for GSM4135986
Status Public on Oct 18, 2020
Title P_AgP25-2
Sample type SRA
 
Source name Pseudomonas aeruginosa PAO1 bacteria
Organism Pseudomonas aeruginosa PAO1
Characteristics strain: PAO1
tissue: liquid M9 culture
Treatment protocol Pseudomonas aeruginosa PAO1 was cultured in 10 mLM9 media containing 0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, at 30 °C, with shaking
Growth protocol liquid M9 culture at 30 °C
Extracted molecule total RNA
Extraction protocol Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
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.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
 
Submission date Oct 23, 2019
Last update date Oct 29, 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
 
Platform ID GPL18782
Series (1)
GSE139104 Next Generation Sequencing Facilitates Quantitative Analysis of Pseudomonas aeruginosa PAO1 Transcriptomes under AgNP and AgNR exposure
Relations
BioSample SAMN13091579
SRA SRX7044150

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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