|
| Status |
Public on Dec 31, 2023 |
| Title |
YAD rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: ZS1
developmental stage: log phase
culture medium: MSM with 2% YE
|
| Treatment protocol |
Cell samples prior to (0h) and after (48h) medium shift were collected by centrifugation at 4000 × g, cells were preserved in liquid nitrogen before extration.
|
| Growth protocol |
All the bacterial cells were grown in MSM medium with either YE or glucose under 30 ℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sample cells using TRIzol Plus RNA Purification System (Invitrogen-Life Technologies Co., Carlsbad, CA, USA) according to manufacturer’s protocol, ribosomal RNA were removed prior to library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
three times subculture in MSM with YE medium, named YE-adapted
|
| Data processing |
Using FastQC v0.11.2 to check the qualities of sequenced reads
Sequenced Reads were removed adaptor-like sequences of 12-nts at the 5’-end and low quality nucleotide with different length at the 3’-end using Trimmomatic v0.32
The resulting sequences with minimal length of 50-nts were mapped to the reference genome P. aeruginosa PAO1 using Bowtie2 v2.2.6 with default parameters
Transcription levels were determined using rsem-calculate-expression to calculate TPM values (-p 6 --bowtie2 --paired-end)
Genome_build: P. aeruginosa PAO1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Nov 26, 2017 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Jianhua Liu |
| E-mail(s) |
liujh2013@zju.edu.cn
|
| Organization name |
Ocean College, Zhejiang University
|
| Street address |
1 Zheda Road, Lin-cheng street
|
| City |
Zhoushan |
| ZIP/Postal code |
316000 |
| Country |
China |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE107343 |
RNA-seq based transcriptional profiling of petroleum sludge-derived Pseudomonas aeruginosa ZS1 strain in response to alteration of growth conditions |
|
| Relations |
| BioSample |
SAMN08099162 |
| SRA |
SRX3422640 |
