|
| Status |
Public on Feb 04, 2022 |
| Title |
WT_15min_afterInd_37C_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria grown in Lauria broth
|
| Organism |
Yersinia pseudotuberculosis |
| Characteristics |
strain: YPIII
genotype: wild type
time (minutes): 15
|
| Treatment protocol |
To reach the virulence induction condition, overnight bacterial cultures were diluted to OD600 0.05 in LB and grown at 26ºC. After 1 h, calcium was depleted by adding EGTA to 5 mM and MgCl2 to 20 mM , and cultures were shifted to 37ºC
|
| Growth protocol |
All strains were routinely grown at 26ºC in LB medium containing kanamycin (50 µg/ml) to the desired OD600.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For isolation and purification of RNA, the Trizol method (Ambion Life Technologies, Carlsbad, CA) and the Direct-zol RNA kit (Zymo Research, USA) were used. To remove unwanted DNA, purified RNA was treated with DNAse for 30 min at room temperature according to the manufacturer’s instructions. RNA quantity was measured by Qubit
RNA libraries were prepared for sequencing using RNA-tag seq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed from 5' and 3' ends until all the adapter and low-quality bases were removed and the sequences passed QC checking by FastQC
Reads were aligned to a reference genome of Y. pseudotuberculosis (accession number NC_010465) using bowtie2 with the unique-mapping option.
Post-mapped read quality checking was done using RseQC, and the numbers of reads for each gene were counted using feaatureCount
Aligned reads were converted to BAM and wig by SAMtool and custom script
Differential gene expression was determined using DEseq2, using the shrinkage estimation of dispersion option (lfcSrink =True) to generate more accurate estimates of differential expression in fold changes
Genome_build: NC_010465
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized counts and differential expression statistics for every gene and every sample
|
| |
|
| Submission date |
Feb 02, 2022 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Maria Fallman |
| Organization name |
Umea university
|
| Department |
Molecular Biology
|
| Lab |
Fallman lab
|
| Street address |
Petrus Laestadius väg
|
| City |
Umea |
| ZIP/Postal code |
907 36 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL28682 |
| Series (1) |
| GSE195976 |
RpoN is required for a functional type III secretion system in Yersinia pseudotuberculosis |
|
| Relations |
| BioSample |
SAMN25598574 |
| SRA |
SRX14022868 |
