|
Status |
Public on Jul 28, 2021 |
Title |
STM815 wt in symbiosis with bean rep1 |
Sample type |
SRA |
|
|
Source name |
Pp STM815 symbiosis
|
Organisms |
Phaseolus vulgaris; Paraburkholderia phymatum STM815 |
Characteristics |
strain: wt growth: nodules harvested 21 days post infection medium: inside bean nodules
|
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 NuGen
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
20150521.A-201505_Bp_nod_n_R1 trimmed (GE)_phym: mapping to STM815 genome 20150521.A-201505_Bp_nod_n_R1 trimmed (GE)_bean: mapping to Pvulgaris genome
|
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); P. vulgaris genome (accession no. GCA_000499845)) Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample
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Submission date |
Jun 07, 2021 |
Last update date |
Jul 28, 2021 |
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 |
GPL30237 |
Series (1) |
GSE176287 |
Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA |
|
Relations |
BioSample |
SAMN19594721 |
SRA |
SRX11083623 |