|
Status |
Public on Dec 01, 2023 |
Title |
CK-3, non-exposed but evolved PAO1 |
Sample type |
SRA |
|
|
Source name |
PAO1
|
Organism |
Pseudomonas aeruginosa |
Characteristics |
strain: PAO1 genotype: CK treatment: non-exposed but evolved PAO1 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 |
SAMN31812211 |
SRA |
SRX18326185 |