|
| Status |
Public on Apr 30, 2022 |
| Title |
37b-R |
| Sample type |
SRA |
| |
|
| Source name |
bacilli
|
| Organism |
Yersinia pestis |
| Characteristics |
strain: Vaccine strain EV76
cell type: bacilli
treatment: Culture at 37 C
|
| Treatment protocol |
EV76 was cultured at 21°C or 37°C with shaking until OD600 reaches 0.5. The bacteria were collected by centrifugation, immediately frozen with liquid nitrogen, and then stored at -80°C. Three biological repeats were performed
|
| Growth protocol |
Y. pestis strains EV76 were grown on Luria-Bertani (LB) broth at 21°C or 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The SV Total RNA Isolation System (Promega, USA) was used to isolate the total RNA and the RNA quality and quantity were checked using Bioanalyzer (Anilent, USA) and RNA 6000 Nano kit (Anilent, USA)
rRNA was removed using the Ribo-Zero rRNA removal kit, followed by the construction of the cDNA libraries and sequencing on an illumona HiSeq 2500 sequencer (Illumina, USA), using paired-end 2- by 150-bp reads. Gene expression changes were measured by the Reads Per Kilobase Per Million Read (FPKM) and the false discovery rate (FDR) (q value). Differentially expressed genes (DEGs) between the 21°C or 37°C culture groups were calculated by DESeq, and a fold change value of 1.5 and a q value of 0.05 was determined as DEGs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 27, 2022 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Lihua Yang |
| E-mail(s) |
wp030801@126.com
|
| Organization name |
Yunnan Institute for Endemic Disease Control and Prevention
|
| Street address |
No. 5, Wenhua Road, Xiaguan Town, Dali Prefecture, Yunnan Province
|
| City |
Dali |
| ZIP/Postal code |
671000 |
| Country |
China |
| |
|
| Platform ID |
GPL23606 |
| Series (1) |
| GSE201684 |
Detection of gene expression level of Yersinia pestis vaccine strain EV76 at 21 and 37 degrees Celsius |
|
| Relations |
| BioSample |
SAMN27914740 |
| SRA |
SRX15014593 |
