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Sample GSM2864999 Query DataSets for GSM2864999
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

Supplementary file Size Download File type/resource
GSM2864999.txt.gz 116.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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