|
| Status |
Public on Jul 11, 2020 |
| Title |
Uninfected Acanthamoeba castellanii_3h_2 |
| Sample type |
SRA |
| |
|
| Source name |
A. castellanii cells
|
| Organism |
Acanthamoeba castellanii |
| Characteristics |
strain: Acanthamoeba castellanii (Neff)
l.pn infection: Uninfected
hours of infection: 3
|
| Treatment protocol |
A. castellanii trophozoites were left uninfected or infected with wild type L. pneumophila or the isogenic DdotA mutant for 3 h, 8 h (early infection), 16 h (mid infection) or 24 h (late infection).
|
| Growth protocol |
2 × 105 A. castellanii were seeded in technical and biological triplicate in PYG medium in 24-well plates (4 × 105 cells per ml) and incubated for 24 h at RT. A. castellanii was then washed with minimal medium to remove non-adherent cells followed by L. pneumophila infection with MOI of 50 (Coil et al., 2008). After 1 h incubation at 37 ℃ with 5% CO2, cells were washed with minimal medium and incubated in fresh PYG medium at 37 ℃ with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For RNA-sequencing analysis RNA was isolated from A. castellanii using TRIsure™ (Bioline) according to manufacturer’s instructions at 3 h, 8 h, 16 h and 24 h post infection.
cDNA library preparation and sequencing was carried out as described previously (Tanaka et al., 2013). Briefly, 1µg RNA was used for poly(A) selection and cDNA libraries were prepared using the Illumina sample preparation kit. 100 base pair paired-end sequencing was performed on the HiSeq 2500 (Illumina) platform, with the use of TruSeq Stranded mRNA LT sample Prep Kit (IIIumina) according to manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sh017
|
| Data processing |
raw fastq files were aligned to the Acanthamoeba castellanii (Neff) genome using Hisat2
reads mapping to genes were counted using featureCounts
differential gene expression analysis was performed using DESeq2
Genome_build: Acanthamoeba castellanii (Neff)
Supplementary_files_format_and_content: raw counts table from featureCounts
|
| |
|
| Submission date |
Jul 10, 2020 |
| Last update date |
Jul 11, 2020 |
| Contact name |
Shivani Pasricha |
| E-mail(s) |
shivani.pasricha@unimelb.edu.au
|
| Organization name |
Peter Doherty Institute
|
| Department |
Microbiology and Immunology
|
| Street address |
792 Elizabeth Street
|
| City |
Melbourne |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL26127 |
| Series (1) |
| GSE154179 |
Legionella pneumophila infection rewires the Acanthamoeba castellanii transcriptome, highlighting a class of sirtuin genes |
|
| Relations |
| BioSample |
SAMN15502432 |
| SRA |
SRX8706687 |
