|
| Status |
Public on Apr 29, 2015 |
| Title |
H111 s54 complemented mutant |
| Sample type |
SRA |
| |
|
| Source name |
Bc H111 planktonic cells
|
| Organism |
Burkholderia cenocepacia H111 |
| Characteristics |
strain: s54 complemented mutant
growth: planktonic cells, OD600 equal 0.5
medium: minimal medium shift experiment (15 mM to 0.3 mM)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . Ds cDNA was produced and nugen librairies obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Bc H111 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample
|
| |
|
| Submission date |
Feb 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gabriella Pessi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Zürich
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zürich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16128 |
| Series (1) |
| GSE66328 |
s54 -dependent response to nitrogen limitation and virulence in Burkholderia cenocepacia H111 |
|
| Relations |
| BioSample |
SAMN03378108 |
| SRA |
SRX891891 |
