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Sample GSM6050680

Query DataSets for GSM6050680

Status

Public on Apr 23, 2022

Title

ryhB-1_2 rep2

Sample type

SRA

Source name

Salmonella strains

Organism

Salmonella enterica subsp. enterica serovar Enteritidis

Characteristics

strain: SE50336
genotype: ryhB-1 KO

Extracted molecule

total RNA

Extraction protocol

S. Enteritidis wild type (WT) strain 50336 and mutants △ryhB-1, △ryhB-2, and △ryhB-1/ryhB-2 were grown overnight in 50 mL of the LB medium with 160 rpm shaking at 37°C under aerobic condition, washed thrice, and re-suspended with iron-limited and nutrient-limited medium. The above prepared bacterial cells were cultured for 2 h at 37°C in the anaerobic workstation. Each sample was analysed in triplicate. Total RNA of the above stains was extracted using TRIzol reagentwith DNase digestion according to the manufacturer’s instruction. Ribosome RNA was removed using a Ribo-Zero rRNA removal kit (Illumina) that leaves the mRNA.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Illumina HiSeq TM2500/MiseqTM software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012)
Assembly: P125109

Submission date

Apr 20, 2022

Last update date

Apr 23, 2022

Contact name

Mengping He

E-mail(s)

mx120190738@yzu.edu.cn

Organization name

Yangzhou university

Street address

Shuangqiao Street