|
| Status |
Public on Jul 27, 2019 |
| Title |
DraR1-1 |
| Sample type |
SRA |
| |
|
| Source name |
WT_bacteria
|
| Organism |
Deinococcus radiodurans |
| Characteristics |
strain background: R1
genotype/variation: wild type
growth phase: OD600≈0.5
|
| Treatment protocol |
Stranis were grown to early exponential phase (OD600≈0.5)
|
| Growth protocol |
All D. radiodurans strains were grown in tryptone glucose yeast extract liquid media (0.5% tryptone, 0.1% glucose and 0.3% yeast extract) at 30 oC with aeration
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Strains were harvested, frozen using liquid nitrogen, and RNA was isolated using Trizol reagent. A total of 3 µg RNA per sample was used as the input material for library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
R1_1
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly (https://www.ncbi.nlm.nih.gov/genome/?term=Deinococcus+radiodurans+R1). Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
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.
Differential expression analysis was performed using the DEGSeq R package (1.18.0)
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias wascorrected. KOBAS software was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Jul 26, 2019 |
| Last update date |
Jul 27, 2019 |
| Contact name |
Shengjie Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Zhejiang University
|
| Street address |
No. 268, Yuhang Tang Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL26971 |
| Series (1) |
| GSE134934 |
N4-cytosine DNA methylation is involved in the maintenance of genomic stability in Deinococcus radiodurans |
|
| Relations |
| BioSample |
SAMN11431349 |
| SRA |
SRX5690275 |
