|
| Status |
Public on Dec 05, 2023 |
| Title |
120_0.1_10 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organisms |
Pseudomonas putida; Escherichia coli |
| Characteristics |
strain 1: E. coli K-12 LE392
strain 2: P. putida KT2440
cell type: Bacteria
treatment: intergeneric conjugation under the exposure of 0.1 mg/L 120 nm PS
|
| Treatment protocol |
Mixed the donor (E. coli K-12 LE392) and intrageneric recipient or intergeneric recipient at a 1:1 ratio in PBS, and incubation in triplicate for 8 h in 0.1 mg/L 20 nm PS, 10 mg/L 20 nm PS, 0.1 mg/L 120 nm PS, 10 mg/L 120 nm PS, 0.1 mg/L 1000 nm PS, 10 mg/L 1000 nm PS, at 25 °C
|
| Growth protocol |
liquid LB culture at 30 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Trizol method
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 A.baylyi ADP1 reference genome (NC_005966.1) 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.
Assembly: NC_000913, NC_002947, L27758
Supplementary files format and content: Excel file includes FPKM values for each sample
Supplementary files format and content: Excel file includes LOG2FC values for each sample
|
| |
|
| Submission date |
Nov 29, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Yuanyuan Kang |
| E-mail(s) |
yuanyuan_kang@outlook.com
|
| Phone |
+8615813855903
|
| Organization name |
Harbin Institue of Technology
|
| Department |
School of Civil and Environmental Engineering
|
| Street address |
No. 6 Pingshan 1st Road, Taoyuan Street, Nanshan District
|
| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL24748 |
| Series (1) |
| GSE248909 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and PS micro-/nanoplastics stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes |
|
| Relations |
| BioSample |
SAMN38498357 |
| SRA |
SRX22677380 |
