|
| Status |
Public on Apr 13, 2018 |
| Title |
EM3016_2 |
| Sample type |
SRA |
| |
|
| Source name |
S. Typhimurium planktonic culture, ΔrfaL
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 |
| Characteristics |
genotype/variation: {delta}rfaL
|
| Treatment protocol |
Cells from 2 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation. The RNA was stored at -70°C.
|
| Growth protocol |
LB medium at 37°C and 140 rpm until OD600=2.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were mapped to the Salmonella_enterica genome (GI:16763390, NC_003197.1) using the Stampy aligner with default settings.
Differential expression was estimated using the R library DESeq
Genome_build: ASM694v1
Supplementary_files_format_and_content: The processed file in .txt format include gene IDs, gene names and reads per gene for each of the samples
|
| |
|
| Submission date |
Sep 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthias Preusse |
| Organization name |
Helmholtz Centre for Infection Research
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22503 |
| Series (1) |
| GSE87447 |
Regulation of flagellum biosynthesis in response to cell envelope stress in Salmonella Typhimurium |
|
| Relations |
| BioSample |
SAMN05833301 |
| SRA |
SRX2195707 |
