|
| Status |
Public on Feb 23, 2018 |
| Title |
STM815 wt nitrogen starved_2 |
| Sample type |
SRA |
| |
|
| Source name |
Pp STM815 planktonic cells
|
| Organism |
Paraburkholderia phymatum STM815 |
| Characteristics |
strain: STM815
genotype: wt
growth phase: planktonic cells, OD600 equal 0.4
growth medium: minimal medium 0.5 mM NH4
|
| 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) . For RNA extracted from nodules, first nodules were disrupted with TissueLyzer and then rRNA of plants was removed using Ribo-zero kit (Epicentre). The cDNA was produced and nugen libraries obtained.
RNA libraries were prepared using Encore Complete Prokaryotic RNA-Seq DR Muliplex System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Pp STM815 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: STM815 genome sequence (accession no. NC_010622.1, NC_010623.1, NC_010625.1 and NC_010627.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample; data exported from CLC
|
| |
|
| Submission date |
Nov 27, 2017 |
| 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 |
GPL22728 |
| Series (1) |
| GSE107381 |
In-nodule transcriptome analysis of Paraburkholderia phymatum during symbiosis with Phaseolus vulgaris |
|
| Relations |
| BioSample |
SAMN08102238 |
| SRA |
SRX3424229 |
