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Sample GSM1547958 Query DataSets for GSM1547958
Status Public on Jan 23, 2016
Title OMV RNA seq.
Sample type SRA
 
Source name OMV
Organism Pseudomonas aeruginosa PAO1
Characteristics cell type: membrane vesicle
media: complex medium LB
Growth protocol P. aeruginosa was grown in LB
Extracted molecule total RNA
Extraction protocol RNA was extracted by the hot phenol method from the cell or purifed OMV
RNA libraries were prepared for sequencing according to the Illumina TruSeq RNA preparation guide
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description condition1
Data processing Illumina Casava1.8 software used for basecalling.
Sequencing reads were mapped to the PAO1 genome (RefSeq NC_002516.2) using CLC Genomics Workbench v4.9 (CLCbio) allowing up to 2 mismatches per read.
RNA-Seq count data were analyzed for differential transcript expressionby the R package DESeq (version 1.6.1, Anders and Huber, 2010).
Supplementary_files_format_and_content: RPKM
 
Submission date Nov 18, 2014
Last update date May 15, 2019
Contact name Masanori Toyofuku
Organization name University of Tsukuba
Street address Tennoudai 1-1-1
City Tsukuba
ZIP/Postal code 305-8572
Country Japan
 
Platform ID GPL19430
Series (1)
GSE63388 RNA-seq. and DNA-seq. of Pseudomonas aeruginosa PAO1 derived membrane vesicles
Relations
BioSample SAMN03198948
SRA SRX761422

Supplementary file Size Download File type/resource
GSM1547958_NG-5812_V2_7756_sequence.txt.gz 191.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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