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| Status |
Public on Jul 04, 2020 |
| Title |
Cobalt treatment_rep1 |
| Sample type |
SRA |
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| Source name |
Co-treated Streptococcus suis
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| Organism |
Streptococcus suis |
| Characteristics |
strain: SC19
treatment: 0.25 mM cobalt, 15 min
growth phase: mid-exponential phase
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| Treatment protocol |
The culture was divided into 3 aliquots, which were supplemented with 2 mM FeSO4, 0.25 mM CoSO4, or H2O, respectively. Following 15 min treatment, bacterial cells were collected for RNA extration.
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| Growth protocol |
Streptococcus suis was grown at 37 °C in Tryptic Soy Broth (TSB) supplemented with 10% (vol/vol) newborn bovine serum. Overnight culture of the strain was diluted 1:100 in fresh medium, and grown to the mid-exponential phase (OD600 = 0.6).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
The transcriptome of Streptococcus suis following treatment with cobalt
Co1
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| Data processing |
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.
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).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Streptococcus suis SC84, complete genome (NC_012924.1).
Supplementary_files_format_and_content: read counts for each gene and each sample.
Supplementary_files_format_and_content: fpkm values for each gene and each sample.
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| Submission date |
Jul 03, 2020 |
| Last update date |
Jul 04, 2020 |
| Contact name |
Chengkun Zheng |
| E-mail(s) |
zhengchengkun@yzu.edu.cn
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| Organization name |
Yangzhou University
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| Street address |
East wenhui road No.48
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| City |
Yangzhou |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL28813 |
| Series (1) |
| GSE153766 |
Transcriptomic analysis of Streptococcus suis in response to ferrous iron and cobalt toxicity |
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| Relations |
| BioSample |
SAMN15438796 |
| SRA |
SRX8664946 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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