|
| Status |
Public on Dec 01, 2023 |
| Title |
ES-2,60-day PtNPs exposed and evolved PAO1 (ES) |
| Sample type |
SRA |
| |
|
| Source name |
PAO1
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
genotype: ES
treatment: 60-day PtNPs exposed and evolved
time: Day 60
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TruSeq™ Stranded Total RNA Library Prep Kit (Illumina, CA, USA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
SeqPrep gram (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) were used to filter the raw reads.
Clean data was mapped with the reference genome of P. aeruginosa (GCA_000006765.1) by Bowtie2
RSEM (http://deweylab.github.io/RSEM/) was utilized for quantification of transcripts expression, and DEseq2 (https://github.com/mikelove/DESeq2) was utilized for identification and analysis of differentially expressed genes (DEGs) among samples (log2FC ≥ 1 and p < 0.05)
Assembly: GCA_000006765.1
Supplementary files format and content: The mRNA abundance was determined by the number of uniquely mapped reads from a transcript per million reads (TPM)
|
| |
|
| Submission date |
Nov 21, 2022 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Yulu Lian |
| E-mail(s) |
20020160048@pop.zjgsu.edu.cn
|
| Phone |
+8619858172692
|
| Organization name |
Zhejiang Gongshang University
|
| Street address |
Hangzhou
|
| City |
Hangzhou,Zhejiang |
| State/province |
Zhejiang |
| ZIP/Postal code |
310035 |
| Country |
China |
| |
|
| Platform ID |
GPL18287 |
| Series (1) |
| GSE218408 |
Effect of long-term exposure of platinum nanopariticles on gene expression of Pseudomonas aeruginosa PAO1 |
|
| Relations |
| BioSample |
SAMN31812209 |
| SRA |
SRX18326187 |
