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| Status |
Public on Nov 28, 2018 |
| Title |
08_h_WT_R1 |
| Sample type |
SRA |
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| Source name |
HeLa cells in fected with S. Typhimurium
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| Organisms |
Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
cell line: HeLa
strain: wild type
time after infection: 8
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| Treatment protocol |
Infection assays were carried out as previously described (Westermann et al., 2016).
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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. 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 |
mirVana kit
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 (Epidemiology) + fragmentation + standard cloning protocol
gene_wise_quantifications_combined_Human_uniquely_only.csv
gene_wise_quantifications_combined_Salmonella_uniquely_only.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: GRCh37, 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) |
foerstner@zbmed.de
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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 |
GPL20051 |
| Series (2) |
| GSE117236 |
Role of ProQ in Salmonella virulence - dual RNA-Seq |
| GSE117256 |
Role of ProQ in Salmonella virulence |
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| Relations |
| BioSample |
SAMN09671199 |
| SRA |
SRX4400366 |
| 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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