|
| Status |
Public on Sep 25, 2019 |
| Title |
yccT mutant_untreated_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells
|
| Organism |
Salmonella enterica subsp. enterica serovar Enteritidis |
| Characteristics |
genotype: Isogenic yccT mutant
treatment: No H2O2 treatment
|
| Treatment protocol |
The Salmonella cultures reaching their mid log growth phase (i.e., OD 600 nm 0.5) were treated with 3 uM of H2O2 followed by centrifugation and washing.
|
| Growth protocol |
Each culture of the wild type and its yccT mutant was inoculated into 100 mL of freshly preapared LB broth followed incubation at 37 C with constant shaking 190 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNAeasy Kit from Qiagen. All bacterial samples were re-suspended in RNAprotect bacterial agent (Qiagen, Valencia, CA, USA) and stored at -20°C until RNA extraction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the S. enterica (P125109) as a reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: S. enterica (P125109)
Supplementary_files_format_and_content: raw read counts
|
| |
|
| Submission date |
Sep 24, 2019 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Sinisa Vidovic |
| E-mail(s) |
svidovic@umn.edu
|
| Phone |
6126263669
|
| Organization name |
University of Minnesota
|
| Street address |
1971 Commonwealth Avenue
|
| City |
Saint Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL27516 |
| Series (1) |
| GSE137933 |
Characterization of novel STY1099 protein involved in the peroxide stress response of Salmonella Enteritidis |
|
| Relations |
| BioSample |
SAMN12830360 |
| SRA |
SRX6895307 |
