Amplicon Sequencing Analysis Dataset / Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs Formalin-Fixated-Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study
Creators: name: Bieri, Uwe
name: Enderlin, Dominik
name: Gadient, Jana
name: Surber, Jonathan
name: Eberli, Daniel
name: Poyet, Cédric
Publisher: name: Zenodo
Year: 2024
Subjects: amplicon sequencing, microbiome, microbial communities, operational taxonomic units (OTUs), taxonomic aggregation, alpha diversity, rarefaction curves, biom data, bladder tissue, fresh frozen, formalin-fixated-paraffin-embedded

description: Amplicon Sequencing Analysis Dataset

Description:This dataset contains the results of an amplicon sequencing analysis performed by Microsynth AG. The data includes quality assessment for each sample, merging reports, unassigned reads, and various analysis results. The analysis results cover OTU (Operational Taxonomic Unit) summaries, taxonomic aggregations, and downstream analysis visualizations.

The dataset is organized into the following main sections:



Quality Assessment: Contains R1 reads, R2 reads, and merged reads for each sample.

MultiQC Summaries: Provides interactive reports for sequencing QC and merged reads QC.

Analysis Results: Includes summaries of OTUs per sample, reads per sample, reads per OTU, OTU fasta info, and OTU table stats. It also contains OTU-related data such as sequences, taxonomies, relative abundance, normalized and reordered abundance, core microbiome, and combined tables. Taxonomic aggregations at various levels (domain, kingdom, phylum, class, order, family, genus, and species) are also provided.

Downstream Analysis Results: Offers visualizations of read distribution, OTU distribution, Krona charts, and sample diversity (alpha diversity, rarefaction curves).

Cleaned biom data: Stored as a phyloseq R data object for further analysis.


This dataset supports the findings of the following study:Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs Formalin-Fixated-Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study

The dataset is suitable for researchers interested in studying microbial communities and their composition using amplicon sequencing techniques. It provides a comprehensive set of analysis results and visualizations to facilitate the interpretation and exploration of the sequencing data. The data can be used to reproduce the results presented in the aforementioned study and to conduct further analyses related to the comparison of fresh frozen and formalin-fixated-paraffin-embedded bladder tissue samples in microbiome research.

Keywords: amplicon sequencing, microbiome, microbial communities, operational taxonomic units (OTUs), taxonomic aggregation, alpha diversity, rarefaction curves, biom data, bladder tissue, fresh frozen, formalin-fixated-paraffin-embedded

File Formats: TSV, FASTA, HTML, PDF, XLSX, R data object

Data Source: Urological Microbiome Research Unit USZ

Data Processing: The data has been processed and analyzed using Microsynth AG's amplicon sequencing analysis pipeline. Quality assessment, merging, OTU clustering, and taxonomic assignments have been performed.

Version: 1.0

Date of Publication: 22.04.2024