Sequencing and Bioinformatic Analysis

Sequencing was performed using the MiSeq™ Personal Sequencing System (Illumina, San Diego, CA, USA) with 2 × 156 bp paired end. The ‘Trim reads’ tool in CLC Genomics Workbench 20.0 (Qiagen, Hilden, Germany) was used to efficiently filter out and remove nucleotides corresponding to primers 515F and Pro-mod-805R. Demultiplexing was performed using the deML package [45 (link)], using zero available mismatches option. Then, read pairs were processed with DADA2 pipeline [46 (link)], according to published.

Free full text: Click here

Ivanova A.Y., Shirokov I.V., Toshchakov S.V., Kozlova A.D., Obolenskaya O.N., Mariasina S.S., Ivlev V.A., Gartseev I.B, & Medvedev O.S. (2023). Effects of Coenzyme Q10 on the Biomarkers (Hydrogen, Methane, SCFA and TMA) and Composition of the Gut Microbiome in Rats. Pharmaceuticals, 16(5), 686.

Publication 2023

MiSeq™ Personal Sequencing System CLC Genomics Workbench 20.0

Nucleotides Primers

Corresponding Organization : National Medical Research Center of Cardiology

Other organizations : Bauman Moscow State Technical University, Kurchatov Institute, Peoples' Friendship University of Russia, MIREA - Russian Technological University

Top 5 similar protocols

Variable analysis

independent variables

Sequencing technology (MiSeq™ Personal Sequencing System)
Primer sequences (515F and Pro-mod-805R)
Demultiplexing method (deML package)
Bioinformatics pipeline (DADA2)

dependent variables

Not explicitly mentioned

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the input protocol.

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!