|
Status |
Public on Dec 31, 2023 |
Title |
Y2G rep2 |
Sample type |
SRA |
|
|
Source name |
whole cells
|
Organism |
Pseudomonas aeruginosa |
Characteristics |
strain: ZS1 developmental stage: log phase culture medium: MSM with 2% Glucose
|
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 |
transfer YE-adapted cells to Glu medium
|
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 |
SAMN08099159 |
SRA |
SRX3422643 |