|
| Status |
Public on Nov 20, 2020 |
| Title |
SL1344 inoculum 2 |
| Sample type |
SRA |
| |
|
| Source name |
Salmonella typhimurium SL1344
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
genotype: pool of EZ-Tn5 transposase (Epicentre) mutants
growth condition: the pool of mutants was grown overnight in LB medium
|
| Growth protocol |
Over-night cultures (LB, 37°C, 220rpm) were either collected (inoculum) and gDNA extracted, or used for infection of RAW.B macrophages. At 20h post-infection the macrophages were lysed, the bacteria were collected and used for gDNA extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted with the phenol-chloroform method.
TraDIS library (Barquist et al., 2016 Bioinformatics)
|
| |
|
| Library strategy |
Tn-Seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
The reads were processed with the Bio-TraDIS Toolkit, using smalt (version 0.7.6)
Transposon read counts per gene were summarized using the tradis_gene_insert_sites script
Infected samples were compared to controls using the tradis_comparison.R script using edgeR
Genome_build: Salmonella reference sequences FQ312003, HE654724, HE654725, HE654726
Supplementary_files_format_and_content: comma separated value file containing the results of comparisons between infection samples and inoculum controls using the Bio-TraDIS Toolkit / edgeR
|
| |
|
| Submission date |
Apr 29, 2020 |
| Last update date |
Nov 20, 2020 |
| Contact name |
Lars Barquist |
| E-mail(s) |
lars.barquist@helmholtz-hiri.de
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2 / Bau D15
|
| City |
Würzburg |
| State/province |
Bayern |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22775 |
| Series (1) |
| GSE149580 |
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence |
|
| Relations |
| BioSample |
SAMN14770873 |
| SRA |
SRX8202730 |
