|
| Status |
Public on Dec 11, 2015 |
| Title |
in vitro ΔpinT 00 h R3 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro infection model
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
infection agent: Salmonella Typhimurium SL1344
|
| Treatment protocol |
Cells were washed twice with PBS and once with SPI-2 medium, diluted 1:50 in pre-warmed SPI-2 medium 24 (defined as t0) and grown further in SPI-2 medium in Erlenmeyer flasks for the indicated time periods.
|
| Growth protocol |
To mimic the early stages of the infection of a host cell in vitro, the indicated Salmonella strains were grown in LB overnight, diluted 1:100 in LB and grown to an OD600 of 2.0 (i.e. a condition under which SPI-1 is highly induced).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRvana kit for total RNA (Ambion)
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 s each). Then, RNAs <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). This was followed by a dephosphorylation with Antarctic Phosphatase (AP, NEB) and re-phosphorylation with T4 Polynucleotide Kinase (PNK, NEB). Oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
total RNA after rRNA depletion
|
| Data processing |
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20 (version 0.0.13)
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0 (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition
|
| |
|
| Submission date |
Dec 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
|
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Information Services
|
| Lab |
Förstner Lab
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21220 |
| Series (2) |
| GSE60144 |
Dual RNA-seq of diverse human, mouse and pig cell-types infected with various Salmonella strains |
| GSE67949 |
Dual RNA-seq – Comparative RNA-seq (in vitro medium shift experiment) |
|
| Relations |
| SRA |
SRX1470899 |
| BioSample |
SAMN04327100 |
