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| Status |
Public on Nov 28, 2018 |
| Title |
dhfq_LB_R3 |
| Sample type |
SRA |
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| Source name |
S. Typhimurium_in-vitro conditions
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| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: hfq mutant
medium: LB
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| Treatment protocol |
Infection assays were carried out as previously described (Westermann et al., 2016). To avoid loss of the proQ overexpression plasmid (and the respective empty control vector) during intracellular bacterial growth, we performed HeLa infection assays in the presence or absence of the respective selection marker (ampicillin) in the host cell medium.
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| Growth protocol |
Salmonella enterica serovar Typhimurium strain SL1344 (strain JVS-1574; (Stocker et al., 1983)) and a constitutively GFP-expressing derivative thereof (JVS-3858; (Papenfort et al., 2009)) are considered as wild-type. Chromosomal mutations were generated as previously described (Datsenko and Wanner, 2000), the respective resistance cassettes eliminated using the FLP helper plasmid pCP20 (Datsenko and Wanner, 2000) at 42°C, and the mutated alleles subsequently transduced into one of the wild-type backgrounds (GFP-negative or –positive, respectively) using P22 phage (Sternberg and Maurer, 1991). For plasmid transformation, the respective Salmonella strains were electroporated with ~10 ng of DNA. The complete lists of bacterial strains and plasmids used in this study are provided in Supplementary Tables S5 and S6. Routinely, Salmonella strains were grown in liquid Lennox broth (LB) medium or on solid LB agar medium at 37°C. When appropriate, liquid or solid media were supplemented with 30 μg/mL chloramphenicol (Cm), 100 μg/mL ampicillin (Amp), 50 μg/mL kanamycin (Kan), or 0.02% (w/vol) L-arabinose (final concentrations).
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol
TruSeq-based (at Vertis Biotech. AG, Freising, Germany)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Ribo-Zero (Bacteria) + fragmentation + standard cloning protocol
gene_wise_quantifications_combined.csv
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| Data processing |
Adaptor removal and quality trimming with cutadapt (version 1.13)
Read mapping with READemption (version 0.4.3) and segemehl (0.2.20)
Feature quantification with READemption (version 0.4.3)
Genome_build: NC_016810.1, NC_017718.1, NC_017720.1
Supplementary_files_format_and_content: reads per feature in csv format (tabular separated)
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| Submission date |
Jul 17, 2018 |
| Last update date |
Nov 28, 2018 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
[email protected]
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| Organization name |
ZB MED - Information Centre for Life Sciences
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| Department |
Information Services
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| Lab |
Förstner Lab
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| Street address |
Gleueler Str. 60
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| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
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| Platform ID |
GPL20056 |
| Series (2) |
| GSE117255 |
Role of ProQ in Salmonella virulence - in vitro |
| GSE117256 |
Role of ProQ in Salmonella virulence |
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| Relations |
| BioSample |
SAMN09681883 |
| SRA |
SRX4401089 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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