|
| Status |
Public on Apr 05, 2018 |
| Title |
H111 ∆hamD 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bc H111 planktonic cells
|
| Organism |
Burkholderia cenocepacia H111 |
| Characteristics |
genotype/variation: hamD mutant
growth phase: planktonic cells, OD600 equal 1
medium: AB minimal medium with glycerol as C-source
|
| 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 libraries 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 2500 |
| |
|
| Description |
20151202.B-353_R1
|
| 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 (Carlier et al. 2014) 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: *.txt: Tab-delimited text files include RPKM and mean values for each sample.
|
| |
|
| Submission date |
Dec 23, 2017 |
| Last update date |
Apr 05, 2018 |
| Contact name |
Gabriella Pessi |
| E-mail(s) |
gabriella.pessi@uzh.ch
|
| Organization name |
University of Zürich
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zürich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL23128 |
| Series (1) |
| GSE97171 |
Biosynthesis of the antifungal compound fragin is controlled by a novel quorum sensing signal |
|
| Relations |
| BioSample |
SAMN08237516 |
| SRA |
SRX3508139 |
