Assays

The experimental data of Midazolam, OH-Midazolam, Caffein, Codeine, Norcodeine, Codein-6Glucuronide, Morphine-3Glucuronide and Morphine was analyzed via a Bayesian uncertainty quantification. An underlying model describing the bolus injection, followed by the exponential decay was written in sbml and a PEtab problem was created. The sampling and ensemble creation was conducted with the python toolbox pyPESTO.

For further details, please take a look at the methods section of the paper.

Stained sections were digitalized using a whole slide scanner (L11600, Hamamatsu, Ja-pan) equipped with the NDP.view2Plus Image viewing software (Version U12388-02).

• MNT-021_J-20-0152_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-022_J-20-0154_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-023_J-20-0156_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-024_J-20-0158_HE_LLL(green), RML(red), RSL (black), ...

Harvest optical densites and methods of transcriptom, proteom and metabolom samples for all tested substrat conditions.

All flux balance analyses of the stoichiometric model

All files for metabolic modeling using the Metano toolbox, including the scenarios and flux balance analyses.

Assay: ASxPv12limmavoomDE-R Short Name: SxPv12limmavoomDE-R Assay Class: DRY Assay Type: R Title: Differential expression analysis of SxPv1.2 data in R Description: Difefrential expression analysis with limma-voom sript in R of total counts from mapping of SxPv1.2 reads to the NbV1 genome. pISA Assay creation date: 2021-11-10 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata20191104.txt Featuredata: Data:

Short Name: 04_SxPv12_GeneSetEnrichment-RNAseg-GSEA Assay Class: DRY Assay Type: RNAseq-GSEA Title: GSEA of SxPv1.2 expression data Description: GSEA anaylysis with MapMan3 BINs as gene sets and SxPv1.2 logFC data. pISA Assay creation date: 2021-11-24 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

Files connected to study: _S_P4_SxP12-newG-DE

Short Name: 03_MapMan-visualisation Assay Class: DRY Assay Type: visualisation Title: Visualisation of DE SxP genes in MapMan. MapMan3 mapping as input. pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: 04_MapManBINenrich-GSEA Assay Class: DRY Assay Type: GSEA Title: GSEA for SxP Illumina mapped reads Description: GSEA of TMM normalized total counts from mapping of SxP Illumina reads to Nb genome v3.5 pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: 05_VOCcomp-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Analysis of VOC data from SxP v1.0 and v1.2 and its comparison to transcriptomic data. Description: Volatile organic compound analysis of young and adult v1.0 and v1.2 high producers was compared to transcriptomic data to gain more insight into the metabolic perturbations in SxP producers. pISA Assay creation date: 2022-01-19 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data: