|
| Status |
Public on Mar 24, 2020 |
| Title |
LPM_DMSO_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
growth media: LPM
treatment group: DMSO
replicate: 2
|
| Treatment protocol |
Samples were treated with DMSO (0.25%) or dephostatin (32 µg/mL) as indicated.
|
| Growth protocol |
Wild-type Salmonella was grown in LB until mid-log phase, then sub-cultured 1:100 into LPM for 5-6 h. 5 mL of each strain was pelleted by centrifugation before RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol-chloroform separation, precipitated with isopropanol, washed with 75% ethanol, then treated with Dnase I.
Purified total RNA was treated with RiboZero for rRNA depletion and strand-specific dUTP sequencing was performed on an Illumina HiSeq 2000 platform to obtain single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw fastq files were trimmed with Cutadapt to remove Truseq adapter sequences
Trimmed reads were aligned against the Salmonella reference genome (NC_016810.1) using BWA (mem algorithm)
Read counts were quantified using featureCounts
DESeq2 was used for differential gene expression analysis
Genome_build: GCF_000210855.2
Supplementary_files_format_and_content: Fastq files contain raw unmapped reads for each sample, txt files contain read counts after alignment
|
| |
|
| Submission date |
Mar 23, 2020 |
| Last update date |
Mar 25, 2020 |
| Contact name |
Brian Coombes |
| E-mail(s) |
coombes@mcmaster.ca
|
| Organization name |
McMaster University
|
| Department |
Biochemistry
|
| Lab |
Coombes
|
| Street address |
MDCL 2108, 1200 Main St W, McMaster University
|
| City |
Hamilton |
| State/province |
ON |
| ZIP/Postal code |
L8N 4L8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17070 |
| Series (1) |
| GSE147414 |
RNA-sequencing of dephostatin-treated Salmonella |
|
| Relations |
| BioSample |
SAMN14428295 |
| SRA |
SRX7973262 |
