|
| Status |
Public on Dec 01, 2023 |
| Title |
A8-1 in MRS at 22h replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
collected the whole fermentation cells
|
| Organism |
Enterococcus durans |
| Characteristics |
genotype: wild type strain A8-1
|
| Treatment protocol |
E. durans A8-1was inoculated into MRS medium with 60 μg/ml Na₂SeO3 and incubated aerobically with constant temperature shaker at 37 °C
|
| Growth protocol |
E. durans A8-1was inoculated into MRS medium and incubated aerobically with constant temperature shaker at 37 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from E. durans A8-1 grown in MRS broth containing 60 μg/ml selenite using a bacteria RNA kit (Tiangen Biotech Co. Ltd, Beijing, China). E. durans A8-1 grown in MRS broth without selenite was used as negative control, the control and treatment were all in triplicates. 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® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Through qualified RNA samples, the cDNA library was constructed, and then transcriptome sequencing was performed at Novogen Co. Ltd (Beijing, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Biological replicate 3 of 3 Enterococcus durans A8-1 strain in MRS medium, 22h culture cells
A8_B.txt
|
| Data processing |
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.
The raw data passed the quality control and mapped to the reference genome, differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value<0.05 found by DESeq were assigned as differentially expressed. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression. For the differentially expressed genes, the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment were analyzed.
Genome_build: PRJNA769572(Enterococcus durans A8-1 )
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 05, 2021 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Bei Han |
| E-mail(s) |
hanbei@mail.xjtu.edu.cn
|
| Organization name |
Xi'an Jiaotong University
|
| Department |
School of Public Health
|
| Street address |
NO 76 Yanta West Road
|
| City |
Xi'an |
| State/province |
Shaanxi |
| ZIP/Postal code |
710061 |
| Country |
China |
| |
|
| Platform ID |
GPL30933 |
| Series (1) |
| GSE188295 |
Next Generation Sequencing Facilitates Quantitative Analysis of Enterococcus durans A8-1 cells fermentation at MRS medium and MRS medium supplied with 60mg/L Na2SeO3 |
|
| Relations |
| BioSample |
SAMN22933716 |
| SRA |
SRX13013980 |
