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Sample GSM6541555

Query DataSets for GSM6541555

Status

Public on Sep 06, 2022

Title

RB1_10_2

Sample type

SRA

Source name

bacterial cells

Organism

Sphingomonas melonis TY

Characteristics

cell type: bacterial cells
treatment: 1% NaCl, 10 min

Treatment protocol

Transcriptome sequencings were carried out on S. melonis TY cultured under three levels of salt stress (0%, 1%, 2%) for 10 or 30 minutes. A total of 18 samples (6 treatments with 3 replicates) were sequenced.

Growth protocol

shake-flask culture, LB culture, 30℃, 200 rpm

Extracted molecule

total RNA

Extraction protocol

Total bacterial samples were collected (A600 = 0.6 at the time of collected), mixed with 0.2 volumes of stop-mix (95% ethanol and 5% phenol, v/v) and snap-frozen in liquid nitrogen. Pellets were resuspended in 100 μl lysozyme solution (15 mg/ml lysozyme in TE buffer, pH = 8.0). Total RNA was isolated with Omega-E.Z.N.A.® Bacterial RNA Kit.
Briefly, RNA degradation and contamination were monitored on 1% agarose gels. The integrity of RNA sample was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, USA). Sequencing libraries were generated from rRNA-depleted RNA using the RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Thermo Scientific, USA) following the manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Before data analysis, raw data were firstly processed through in-house perl scripts as a quality control. Demultiplexed and quality filtered reads were then aligned to S. melonis TY genome sequence using Bowtie2-2.2.3. HTSeq 0.6.1 was used to count the reads numbers mapped to each gene.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 3000

Data processing

Raw data were firstly processed through in-house perl scripts as a quality control. Demultiplexed and quality filtered reads were then aligned to S. melonis TY genome sequence using Bowtie2-2.2.3. HTSeq 0.6.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq Rpackage (1.18.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: ASM176134v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

Submission date

Sep 02, 2022

Last update date

Sep 21, 2022

Contact name

Xiaoyu Wang

E-mail(s)

[email protected]

Phone

18894038858

Organization name

Zhejiang University