|
| Status |
Public on May 01, 2021 |
| Title |
Salmonella control culture replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Free-living Salmonella culture in PAS medium
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 |
| Characteristics |
strain: 14028S
condition: control
sample type: Free-living Salmonella culture
|
| Treatment protocol |
The Salmonella cells were added to the Acanthamoeba culture in sterile PAS at a 100:1 bacterium:amoeba ratio. The co-culture was incubated for 1 h until most of the bacteria had been ingested by the Acanthamoeba. The suspension was then washed thrice with PAS to remove extracellular bacteria. The co-cultures were then centrifuged at 800g for 5 min at 25 °C, the supernatants were transferred to sterile tubes, and the pellets were resuspended in 1 mL ExtractRNA reagent (Evrogen, Moscow, Russia).
|
| Growth protocol |
Salmonella was grown in Luria broth at 37°C without antibiotics. A. castellanii axenic culture was grown for 5 d in PYG medium to a density of 4-5 × 10^5 cells/mL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with ExtractRNA reagent (Evrogen, Moscow, Russia). The RNA samples were treated with a TURBO DNA-free™ kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions. The RNA content was determined in a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity, purity, and concentration were assessed with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
The Cappable-Seq procedure was performed as previously described [Ettwiller et al., 2016].
Cappable-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
VCE_S2
|
| Data processing |
Demultiplexed reads were trimmed against adapters with bbduk.
SortMeRNA was used to remove reads belonging to prokaryote and eukaryote rRNA sequences.
Clean reads were initially mapped against the full A. castellanii genome (GCF_000313135.1) with Bowtie2 [78] in local mode (L-16) and then mapped against the S. Typhimurium 14028s genome (GCA_000022165.1).
The reads per operon were evaluated with featureCounts in the Rsubread package of R.
Genome_build: GCA_000022165.1
Supplementary_files_format_and_content: Operon_count_matrix.csv (Tabular file include operon coverage values for each sample .)
RNA-Seq_stat.xlsx (base statistics)
|
| |
|
| Submission date |
Apr 30, 2021 |
| Last update date |
May 02, 2021 |
| Contact name |
Alexander S Balkin |
| E-mail(s) |
[email protected]
|
| Phone |
0079096071417
|
| Organization name |
Institute for Cellular and Intracellular Symbiosis
|
| Lab |
Laboratory og Biomedical technologies
|
| Street address |
11 Pionerskaya st.
|
| City |
Orenburg |
| ZIP/Postal code |
460000 |
| Country |
Russia |
| |
|
| Platform ID |
GPL20792 |
| Series (1) |
| GSE173638 |
Transcriptome of Salmonella within Acanthamoeba |
|
| Relations |
| BioSample |
SAMN18929577 |
| SRA |
SRX10722140 |
