|
| Status |
Public on Jun 28, 2024 |
| Title |
A. castellanii_C.jejuni_2 |
| Sample type |
SRA |
| |
|
| Source name |
Eukaryotic
|
| Organism |
Acanthamoeba castellanii |
| Characteristics |
tissue: Eukaryotic
cell line: Infected
|
| Treatment protocol |
RNA-Seq was used to identify differentially expressed genes between A. castellanii infected with C. jejuni strain 11168H and uninfected control (which was incubated in the absence of bacteria) after a total of 4 h. Experiments were performed as described above; briefly, A. castellanii 106 were infected with C. jejuni 11168H (M.O.I of 200) for 3 h and washed three times to remove extracellular bacteria. Gentamycin was added to a final concentration of 100 μg/mL; this culture was incubated for a further 1 h before washing three times
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Triazole (Sigma Aldrich, England, UK) following manufacturer’s protocol.
Total RNA was sent out to Genewiz (Azenta) for processing using illumina kits following manufactures protocol.
This was conducted according to illumina protocol by Genewiz (Azenta).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The paired-end reads were trimmed and filtered using Conda; Kallisto was used to map the reads against the reference sequence, Genome assembly Acastellanii.strNEFF v1 GCA_000313135.1. Kallisto was also used to convert annotations from GFF to GTF format. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as metadata associated with the study (multifactorial design). Adjusted p-value significance cut-off of <0.05, and log fold change cut-off of >2, was used for multiple comparison.
Assembly: Genome assembly Acastellanii.strNEFF v1 GCA_000313135.1.
Supplementary files format and content: abundance.tsv. Files contain "target_id" "length" "eff_length" "est_counts" "tpm"
|
| |
|
| Submission date |
Mar 29, 2024 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Fauzy Nasher |
| E-mail(s) |
fauzynasher@gmail.com
|
| Phone |
07867898271
|
| Organization name |
London School of Htgiene and Tropical Medicine
|
| Street address |
London School Of Hygiene & Tropical Medicine, Keppel Street
|
| City |
LONDON |
| State/province |
Please select |
| ZIP/Postal code |
WC1E 7HT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL34348 |
| Series (1) |
| GSE262802 |
Acanthamoeba castellanii as a model for unveiling Campylobacter jejuni host-pathogen dynamics |
|
| Relations |
| BioSample |
SAMN40653784 |
| SRA |
SRX24098567 |
