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Sample GSM4874062

Query DataSets for GSM4874062

Status

Public on Oct 01, 2021

Title

S12_30min_2

Sample type

SRA

Source name

S12_30min

Organism

Shewanella decolorationis

Characteristics

strain: S12
taxonomy: Gammaproteobacteria
treatment: untreated
treatment duration: 30 min

Treatment protocol

Fe0 (60 mM) was added into the defined medium inoculated with the S12 cells. Cell samples were collected from three independent experiments grown with Fe0 condition and without Fe0 condition for 10, 30, 60, 120 min, respectively, and centrifuged at 80,000×g for 10 min at 4°C

Growth protocol

Shewanella decolorationis S12 was grown to a defined medium (pH 7.0) containing 7.64 g/L Na2HPO4, 3.00 g/L KH2PO4, 0.50 g/L NH4Cl, 1.00 g/L NaCl, 5.00 mmol/L sodium lactate, 0.5 g/L yeast extract, 1 mmol/L amaranth and statically cultivated at 30°C in anaerobic workstation (BugBox, Ruskinn Technologies).

Extracted molecule

total RNA

Extraction protocol

Total RNA from the cell pellet was isolated using a TRIzol Reagent kit (Invitrogen, Carlsbad, USA) following the manufacturer’s instructions. RNA samples were treated with RNase-free DNaseI (QIAGEN, Carlsbad, USA) to digest residual genomic DNA and then purified by an RNeasy kit (Qiagen, Valencia, USA). Ribosomal RNA was removed by a RiboZero™ rRNA Removal kit (Epicenter, Madison, USA) following the manufacturer’s protocols (Bhagwat et al., 2014).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

After sequencing, four steps were taken to get a clean reads dataset with high quality. (1) Remove the reads with excess of "N"; (2) eliminate the reads caused by adapter contamination; (3) get rid of the reads that have more than 36 bases with low quality (quality score < 20); (4) Wipe away the duplicated reads generated by PCR amplification.
The clean data were mapped on the annotated genomic objects identified in the genome of S. decolorationis S12 using Tophat 2.0.11 and samtools 0.1.18.0, yielding BAM files (Trapnell et al., 2012; Li et al., 2009).
Sorted and indexed BAM files were analyzed by Cufflinks 2.0.0 (Trapnell et al., 2010) to calculate the number of fragments per kilobase of transcript permillion mapped reads (FPKM) for all genes and thereby detect differentially expressed genes.
Based on the calculations made by Cuffdiff, genes with |log2 fold changes (filamentous verse normal cell)| > 1 and FDR-p value < 0.05 were marked as significant.
Genome_build: AXZL01000000 (Shewanella decolorationis S12)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

Submission date

Oct 30, 2020

Last update date

Oct 01, 2021

Contact name

Yun Fang

E-mail(s)

fangyun1987@126.com

Organization name

Guangdong Institute of Microbiology

Street address

100 Central Xianlie Road