Presence of M. globosa DNA within pancreatic FFPEs

This record contains supporting data used to assess the presence of Malassezia globosa in pancreatic formalin-fixed paraffin-embedded (FFPE) tissue. It combines TaqMan quantitative PCR (qPCR) results and available fluorescence in situ hybridization (FISH) counts with DNA sequencing–based microbial profiles and accompanying metadata. The dataset supports the associated manuscript and allows readers to inspect the underlying Cq values, FISH counts, microbial abundance profiles, and sample-level annotations.

Contents

qPCR and FISH

TaqMan qPCR M. globosa in pancreatic tissue_version2.xlsx – qPCR table for M. globosa and human beta-globin/HBB in pancreatic FFPE tissue specimens, including clinical diagnosis, tissue compartment, tissue histology, final M. globosa positivity calls, and available FISH counts.

README_Zenodo_Mglobosa_qPCR_v2.txt – README explaining the qPCR/FISH dataset structure, compact spreadsheet layout, technical replicate rows, interpretation of “No Cq”, positivity threshold, and calculation of derived variables such as ΔCt and relative 2^-ΔCt burden.

simple_data_dictionary_v2.csv – Simple data dictionary listing the variables in the qPCR/FISH workbook and providing brief descriptions.

Sequencing

DNA_Sequencing_MicrobialCounts.numbers – Microbial count table derived from DNA sequencing of pancreatic FFPE tissue specimens.

DNA_Sequencing_Metadata.numbers – Sample-level metadata corresponding to the DNA sequencing microbial count table.

DNA_Sequencing_Unmapped_Fastq.zip – Compressed archive containing unmapped FASTQ files from the DNA sequencing runs.

Workbook info

qPCR workbook sheet: Tabelle1

Main qPCR sheet used for the manuscript: Tabelle1

How to interpret the qPCR data

Lower Cq values indicate higher target abundance. “No Cq” indicates no detectable amplification within the qPCR cycling limit. For the continuous relative-burden analyses reported in the manuscript, samples without detectable M. globosa amplification were assigned Cq = 40, and relative fungal burden was calculated as 2^-ΔCt, where ΔCt = Cq(M. globosa) − Cq(HBB). M. globosa positivity was defined according to the manuscript-specified reproducibility criteria and predefined Cq threshold.

How to link the files

Sample identifiers and metadata can be used to relate qPCR/FISH results, microbial count data, and sequencing metadata where applicable. For the full analytical workflow, quality-control procedures, and statistical analyses, please refer to the associated manuscript and the README file.

Methods, plain language

qPCR: TaqMan qPCR was used to detect M. globosa DNA and human beta-globin/HBB in pancreatic FFPE tissue. HBB served as the human DNA reference and quality-control marker.

FISH: Fluorescence in situ hybridization was used for probe-based visualization of M. globosa signals in selected specimens. Available FISH counts are reported in the qPCR workbook.

DNA sequencing: DNA sequencing–based microbial profiles, corresponding metadata, and unmapped FASTQ files are provided to support re-analysis of the sequencing component of the study. Library preparation, read processing, and taxonomic assignment are described in the associated manuscript.

Keywords

qPCR; TaqMan; Malassezia globosa; beta-globin; HBB; FFPE; pancreas; pancreatic ductal adenocarcinoma; precursor lesions; Cq; FISH; fluorescence in situ hybridization; DNA sequencing; microbial counts; unmapped reads; metadata

License

Creative Commons Attribution 4.0 International (CC BY 4.0).

Contact

For questions about the data, please contact the corresponding author.