|
| Status |
Public on Dec 11, 2015 |
| Title |
3D4 31 ΔpinT 16 h replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
cell culture infection model
|
| Organisms |
Sus scrofa; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
pig cell line: 3D4/31
infection agent: Salmonella Typhimurium SL1344
organism: mixed sample: pig cell line 3D4/31 and Salmonella Typhimurium SL1344
|
| Treatment protocol |
Infection samples: In vitro infection was carried out following the protocol of (Schulte et al., 2011) with the indicated Salmonella Typhimurium (SL1344) strain in 6-well format. At the indicated time point post-infection, cells were fixed with RNAlater (Qiagen) and sorted for invaded (GFP+) and non-infected (GFP-) host cells using a FACSAria III device (BD). Total RNA from the sorted cells was extracted following the miRvana protocol (Ambion). "0 h" refers to RNA extracted from mixed lysates of extracellular Salmonella and host cells.
|
| Growth protocol |
Host cells were cultured according the guidelines provided by the ENCODE consortium (http://genome.ucsc.edu/encode/protocols/cell/human/Stam_15_protocols.pdf). Cells were grown in DMEM (Gibco) supplemented with 10% fetal calf serum (FCS; Biochrom), 2 mM L-glutamine (Gibco) and 1 mM sodium pyruvate (Gibco) in T-75 flasks (Corning) in a 5% CO2, humidified atmosphere at 37°C. All further cell lines used in this study (THP-1, CaCo-2, AGS, HEK, MEF and RAW264.7) were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C.For the differentiation of bone marrow derived macrophages the marrow of femur and tibia was isolated from 8-12 week old female C57BL/6 wild-type mice and stored in RPMI supplemented with 10% FCS. The cell suspension was centrifuged for 5 min at 250 g and the leukocyte pellet was resuspended in differentiation medium consisting of X-vivo-15 medium (Lonza) supplemented with 10% FCS and 10% L929 conditioned DMEM medium (same composition as above). Cells were cultured for 3 days at 3*106 cells per 10 mL in a T-75 flask. At day 3 another 3 mL of differentiation medium were added and cells were further cultured until day 5. Successful macrophage differentiation was validated by microscopy on day 5 upon which the cells were disattached using a rubber scraper (Sarstedt) and seeded into 6-well plates at 105 cells per well in fresh differentiation medium. Infection was carried out on day 7 as described below.
|
| 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
3D4_31:DeltapinT:16_h:R2
|
| 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: Pig: Sscrofa10.2; 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 07, 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 |
GPL20065 |
| Series (2) |
| GSE60144 |
Dual RNA-seq of diverse human, mouse and pig cell-types infected with various Salmonella strains |
| GSE67948 |
Dual RNA-seq – Comparative Dual RNA-seq in pig macrophages |
|
| Relations |
| BioSample |
SAMN04324040 |
| SRA |
SRX1469712 |
