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9 results for “Acanthamoeba castellanii”
Pseudomonas aeruginosa secretes compounds that kill Acanthamoeba castellanii trophozoites
<p>Microscopy of A. castellanii trophozoites incubated with cell-free supernatant from P. aeruginosa strain PA14 overnight cultures in LB. Time elapsed 2 hours. Video acquired using a Canon Vixia HFS200 camera and Nikon Eclipse TS100 microscope (20x objective).</p>
Acanthamoeba castellanii genome assembly and infection by Legionella pneumophila
<p>Data associated with the publication "<em>Regulation of the Acanthamoeba castellanii genome upon infection by Legionella pneumophila</em>". The record contains 4 archives, each associated with a github repository, and a "shared assets" archive, which contains processed files used by some repositories. The code from github repositories is embedded in each tarball, along with input and output data. Analyses are organized as independent snakemake pipelines for each part.</p> <p> </p> <p>For convenient reanalysis, genomes, annotations and merged contact maps used in the publication can be found in the `shared_assets.tar.gz` archive. The infection analysis results are located in the `data/output` folder of Acastellanii_legionella_infection.tar.gz.</p> <p>All archives can be downloaded at the bottom of the page.</p> <p> </p> <p><strong>Hybrid genome assembly:</strong></p> <p>Genome assembly pipeline code and output data used for the assembly of 2 <em>A. castellanii</em> strains (Neff and C3) through a hybrid pipeline combining Illumina shotgun, Hi-C and Oxford Nanopore long reads.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_hybrid_assembly">https://github.com/cmdoret/Acastellanii_hybrid_assembly</a></p> <p>Archive: Acastellanii_hybrid_assembly.tar.gz</p> <p> </p> <p><strong>Genome annotation:</strong></p> <p>Genome annotation pipeline used for functional annotation of <em>A. castellanii</em> strains C3 and Neff, and associated output files.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_genome_annotation">https://github.com/cmdoret/Acastellanii_genome_annotation</a></p> <p>Archive: Acastellanii_genome_annotation.tar.gz</p> <p> </p> <p><strong>Genome analyses:</strong></p> <p>Code and data related to general analyses of genomic properties of <em>A. castellanii</em> strains C3 and Neff.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_genome_analysis">https://github.com/cmdoret/Acastellanii_genome_analysis</a></p> <p>Archive: Acastellanii_genome_analysis.tar.gz</p> <p> </p> <p><strong>Infection analyses:</strong></p> <p>Code and data related to the analysis of structural changes in the <em>A. castellanii</em> C3 genome during infection by <em>L. pneumophila</em>.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_legionella_infection">https://github.com/cmdoret/Acastellanii_legionella_infection</a></p> <p>Archive: Acastellanii_legionella_infection.tar.gz<br> </p> <p><strong>Shared assets:</strong></p> <p>This archive contains processed files (genomes, annotations, Hi-C matrices, differential expression results) which can be useful for reanalysis, and are automatically pulled when executing the pipeline of some repositories.</p> <p>Archive: shared_assets.tar.gz</p> <p> </p> <p><strong>Supp. analyses:</strong></p> <p>Code and data related to short ad-hoc analyses on the genomic location of specific sequences in the genomes of C3 and Neff. The archive contains two subfolders: `telomere_repeats` where we analyse the distribution of TTAGGG subtelomeric repeats throughout the A. castellanii assemblies, and `C3_exclusive_regions` where we visualize the genomic distribution of C3-specific sequences (i.e. absent from Neff) along the C3 assembly.</p> <p> </p> <p>Archive: supp_analyses.tar.gz<br> </p>
Campylobacter jejuni interactions with Acanthamoeba castellanii
GEO Series GSE206909. Campylobacter jejuni; Acanthamoeba castellanii. 6 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome RNA Sequencing Data Set of Differential Gene Expression in Salmonella enterica serovar Typhimurium 14028S within Acanthamoeba castellanii, and under Oxidative and Starvation Stress Condi
GEO Series GSE270532. Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028. 22 samples. Type: Expression profiling by high throughput sequencing.
The transcriptional response of Cryptococcus neoformans to ingestion by Acanthamoeba castellanii and murine macrophages
GEO Series GSE45027. Cryptococcus neoformans. 12 samples. Type: Expression profiling by array.
Legionella pneumophila infection rewires the Acanthamoeba castellanii transcriptome, highlighting a class of sirtuin genes
GEO Series GSE154179. Acanthamoeba castellanii. 36 samples. Type: Expression profiling by high throughput sequencing.
Acanthamoeba castellanii as a model for unveiling Campylobacter jejuni host-pathogen dynamics
GEO Series GSE262802. Acanthamoeba castellanii. 6 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome Cappable-Seq Sequencing Data Set of Gene Expression in Salmonella enterica serovar Typhimurium 14028S inside Acanthamoeba castellanii, and under Oxidative and Starvation Stress Condition
GEO Series GSE271311. Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S. 20 samples. Type: Expression profiling by high throughput sequencing.
Gene expression of Acanthamoeba castellanii under long-term co-culture condition
GEO Series GSE227112. Acanthamoeba castellanii. 2 samples. Type: Expression profiling by high throughput sequencing.
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