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Sample GSM7670498

Query DataSets for GSM7670498

Status

Public on Dec 11, 2023

Title

UY031, water, biol rep 2

Sample type

SRA

Source name

UY031

Organism

Ralstonia solanacearum

Characteristics

strain: UY031
genotype: wt
condition: water

Growth protocol

For the soil samples, a natural soil (Table S2) was autoclaved three times (∼3 h), 200 g of soil was added to pots without plants and incubated for 3 days at plant infection conditions. Finally, 5 g soil samples were sampled. For the water samples, bacteria were recovered 48 h after growth in rich B medium plates, washed and resuspended in sterile mineral water (Water A - Table S1) to a final concentration of ∼107 CFU/mL in 250 mL. The suspension was incubated at 28 °C for 6 hours, centrifuged at 4 ºC, and the pellet frozen in liquid nitrogen.

Extracted molecule

total RNA

Extraction protocol

Total RNA from bacterial pellets grown in water was extracted using the SV Total RNA Isolation System kit (Promega
Total RNA was extracted using the SV Total RNA Isolation System kit (Promega) for water samples and the RNA PowerSoil® Total RNA Isolation Kit (MO BIO) followed with a rigorous DNAse treatment with the TURBO DNA-free kit (Life Technologies) for soil samples.
Bacterial rRNA was removed using NEBNext rRNA Depletion kit (Bacteria) (NEB). Libraries were independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

AM0004_water13_ribo00920_S160922_ACTGAT

Data processing

Samples were trimmed with trimGalore (v.0.6.1) (Moskvin et al., 2011) with the paired (--paired) option to remove adaptors and low quality reads from the analysis
Trimmed libraries were searched for potential contaminants using the software SortMeRNA (v.4.2.0) (Kopylova, Noé and Touzet, 2012) with the default parameters and contaminant libraries
Filtered sequenced reads were mapped to UY031 genome with Bowtie2 (v. 2.4.4) (Langmead and Salzberg, 2013) with deafault parameters.
Raw counts were extracted from alinged files using the prokaryote counting software FADU (Feature Aggregate Depth Utility) (v. 1.8) (Fraser et al., 2021)
Assembly: GCF_001299555.1_ASM129955v1
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes Deseq2 normalized counts for each sample

Submission date

Jul 31, 2023

Last update date

Dec 11, 2023

Contact name

Marc Valls

E-mail(s)

marcvalls@ub.edu, mercerf93@gmail.com

Organization name

CRAG

Lab

Bacterial plant diseases and plant cell death