Disclaimer

RNA-seq

The transcriptomics data is based on deep sequencing of RNA libraries. The library preparation and data analysis will unavoidably introduce biases and errors for a small number of genes. While these errors are rare, it is important to take notice when studying affected genes, since they will cause discrepancies between presented RNA and protein data.

Normalization and classification

When processing transcriptomic data normalization is necessary for comparison between genes and between tissues. The strategy is carefully evaluated by the bioinformatics team, however alternative methods can of cause be used. The classification methods used in the portal is created as tools for understanding the expression landscape, but since cut offs are applied there are rare cases where genes with low expression results in a category not optimal. The optimal cut off is complex and possibly tissue type dependent. The UMAP cluster-based classification is grouping genes based on the expression profile regardless of the cut off or arbitrary category rules. We think that the two different strategies complement each other since all methods have pros and cons.

Tissue sampling

The four animals were sampled by the same team and in similar manner. Brain samples were taken from one hemisphere while the other hemisphere was fixed in formalin for later protein analysis. Peripheral tissue samples were divided into two pieces where one was frozen for RNA extraction and the other adjacent piece was submerged into formalin for fixation, enabling morphological verification and quality assessment. Although the tissue sample was divided into two we cannot know for sure what the sequenced sample included regarding detailed cellular composition.

Immunohistochemistry

Quality assured antibodies have been used in this study and specially educated personnel have evaluated each image. The antibodies used for staining pig tissues was generated to specifically target human genes, although sequence homology was one of the criteria for selecting relevant antibodies to test, it is possible that there are species difference in protein details. Selected antibodies were first confirmed on human tissues, reproducing the online human staining profile, before applied on the pig tissue, using the exact same pretreatment and staining protocol used for the human tissues within the HPA standardized pipeline.