|
| Status |
Public on Oct 26, 2017 |
| Title |
Cells at aw 0.11 |
| Sample type |
SRA |
| |
|
| Source name |
Biological replicate 1, 2, and 3
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 |
| Characteristics |
serovar: Typhimurium
strain: ATCC 14028
|
| Treatment protocol |
Cells were allowed to air-dry for 24 h at room temperature. Filters were placed in desiccators containing water or a saturated solution of lithium chloride 99% (Acros Organics, Thermo Fisher Scientific, Waltham, MA) to allow equilibration to aw 1.0 and 0.11 respectively. Filters were kept in the desiccators for 4 days at 25°C.
|
| Growth protocol |
Working cultures of Salmonella Typhimurium ATCC14028 were freshly inoculated in TSB and grown for 3 h at 37°C shaking at 250 rpm. The cultures were collected through centrifugation (10 min at 5,000×g) and washed twice with distilled sterile water (DSW) to eliminate nutrient residues. Approximately 10^9 CFU were spotted on 0.2 µm polycarbonate filters (Merck Millipore Ltd., Billerica, MA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from Salmonella cells using the RNAprotect Bacteria Reagent and RNeasy Mini Kit (Qiagen, Hilden, Germany). The experiments were repeated three times in different days. Each time, three technical replicates were performed. The total RNA was extracted individually for each replicate and then the RNA was pooled together from all the replicates for the same conditions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
cells equilibrated to aw 0.11
|
| Data processing |
Base call files for each cycle of sequencing were generated by Real-Time Analysis software (Illumina Inc., San Diego, CA). Primary analysis and de-multiplexing were performed using CASAVA software v1.8.2 (Illumina Inc., San Diego, CA).
The reads ends were trimmed using the Auto trim option available in the DNASTAR software package. The ends were trimmed to best match the alignment to the template. SeqMan Ngen marked the portion of the read that aligns well to the template and set the trimming to skip any of the poorly aligned portions of the read.
RPKM (reads assigned per kilobase of target per million mapped reads) normalization was applied. Briefly, the signal values for each experiment were divided by the totaltarget sequence divided by one thousands; and the resulting number divided by the total number of reads divided by the total number of mapped reads divided by one million.
Genome_build: Salmonella enterica serovar Typhimurium strain LT2
|
| |
|
| Submission date |
Sep 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Cristiano Fink |
| E-mail(s) |
[email protected]
|
| Organization name |
St. Cloud State University
|
| Department |
Biology
|
| Lab |
Ryan C. Fink
|
| Street address |
720 4th Ave S
|
| City |
St. Cloud |
| State/province |
MN |
| ZIP/Postal code |
56301 |
| Country |
USA |
| |
|
| Platform ID |
GPL20792 |
| Series (1) |
| GSE86580 |
General response of Salmonella enterica serovar Typhimurium to desiccation: A new role for the virulence factors sopD and sseD in survival. |
|
| Relations |
| BioSample |
SAMN05751872 |
| SRA |
SRX2148414 |
