Protocol detail

Genome and Transcriptome Analysis of Parasite P. dicentrarchi

Find Similar Protocols

For analysis of the P. dicentrarchi genome and transcriptome, trophonts (10⁷) were concentrated by centrifugation, frozen in liquid nitrogen and sent on dry ice to Future Genomic Technologies (Leiden, Netherlands). For sequencing of the complete genome of the ciliate, a combination of short reading sequencing (Illumina technology) and long reading sequencing (Nanopore technology) was used (Oxford Nanopore Technologies). For de novo assembly of the parasite genome, the data sets were combined using the TULIP program v0.4^{40 (link)}. Transcript sequences from Illumina RNA- Seq data (fragments of approximately 100 bp), obtained by amplification by SBS, were assembled using Trinity software (v2.6.5)^{41 (link)}, included within the Galaxy application (https://usegalaxy.org/). The assembled sequences were analyzed by homology, with Blastgo 5.0 software (Biobam, Spain), and annotated. The sequences that encode proteins that are potentially related to the ciliate AOX were then selected from the Tetrahymena thermophila gene and protein sequences database by using the BLASTx tool Wiki TGD (https://www.ciliate.org/blast/blast_link.cgi).

Free full text: Click here

Folgueira I., Lamas J., Sueiro R.A, & Leiro J.M. (2020). Molecular characterization and gene expression modulation of the alternative oxidase in a scuticociliate parasite by hypoxia and mitochondrial respiration inhibitors. Scientific Reports, 10, 11880.

Publication 2020

RNA- Seq data

Bp 100 Centrifugation Ciliate Dry ice Frozen Gene Genome Nitrogen Parasite Proteins Rna seq Tetrahymena thermophila Transcriptome Tulip

Top 5 similar protocols

Protocol cited in 1 other protocol

Variable analysis

independent variables

Sequencing technology (Illumina short-read and Nanopore long-read)

dependent variables

Genome assembly quality
Transcriptome assembly quality

control variables

Trophont cell concentration (10^7 cells)
RNA-Seq fragment size (approximately 100 bp)

controls

Positive control: None specified
Negative control: None specified

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!