|
| Status |
Public on Sep 18, 2018 |
| Title |
STM_minus_3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
genetic background: ∆ssrAB
plasmid: pWSK129
|
| Growth protocol |
Overnight bacterial cultures were sub-cultured 1:50 in LB-kanamycin and grown at shaking for 2.5 hours. These were then sub-cultured 1:50 into LPM pH 5.8 and grown to mid log (OD600=0.4-0.5). Bacteria were then pelleted by centrifugation for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol-chloroform separation, precipitated with isopropanol, washed with 75% ethanol, resuspended in water for Dnase I treatment for 30 min. Dnase I was inactivated with inactivation beads and RNA was re-precipitated with isopropanol, washed with 75% ethanol, and resuspended in water
RNA was rRNA depleted with RiboZero, and strand specific dUTP sequencing was performed on an Illumina Hi-Seq following standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: NC_016810_transcripts.txt
processed data file: NC_017718_transcripts.txt
processed data file: NC_017719_transcripts.txt
processed data file: NC_017720_transcripts.txt
|
| Data processing |
Multiple files for each sample were concatenated into a single file. SsrB- and SsrB+ files for each species were loaded on to Rockhopper for alignment to the referene genome and plasmids if applicable.
Genome_build: Reference genome for S. bongori NC_015761. Reference genome for S. Typhimurium NC_016810. Reference for S. Typhimurium plasmids NC_017718 (pCol1B9), NC_017719 (pRSF), NC_017720 (pSLT)
Reads were mapped to the respective genomes with Rockhopper and differential gene expression (SsrB+/SsrB-) was calculated for both species.
|
| |
|
| Submission date |
Sep 17, 2018 |
| Last update date |
Sep 18, 2018 |
| Contact name |
Brian Coombes |
| E-mail(s) |
coombes@mcmaster.ca
|
| Phone |
905 525 9140
|
| Organization name |
McMaster University
|
| Department |
Biochemistry and Biomedical Sciences
|
| 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) |
| GSE120043 |
RNA-sequencing of SsrB-dependent gene expression in S. Typhimurium and S. bongori |
|
| Relations |
| BioSample |
SAMN10077655 |
| SRA |
SRX4702829 |
