|
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 |