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Supplementary data: Non-destructive extraction of DNA from preserved tissues in medical collections

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posted on 2022-01-17, 10:23 authored by Enrique Rayo, Giada Ferrari, Judith Neukamm, Gülfirde Akgül, Abagail M. Breidenstein, Martyn Cooke, Carina PhillipsCarina Phillips, Abigail S. Bouwman, Frank J Rühli, Verena J. Schuenemann

Supplementary Note 1 - Laboratory workflow

Supplementary Note 2 – Analysis

Supplementary Note 3 – Results

Supplementary Note 4 - Extended Sample Information

Table SI.1: List of tissue and fixative samples utilized in this study. The range of 1760-1793 corresponds to the span when John Hunter (born 1728, died 1793) created his collection.

* Based on the jar lid sealing, these samples have not undergone recent conservation, i.e. the fixative was not recently replaced.

Table SI.2: Primer list: Primers used for the bait design of the Treponema pallidum hybridization-capture protocol.

Table SI.3: Long-range PCR reaction for the generation of baits.

Table SI.4: Temperature settings for the LR-PCR

Table SI.5: Shotgun screening for mtDNA, indicating the cluster factor and the percentage of coverage (1X and 5X).

Table SI.6: Endogenous content of the mtDNA present in the tissue samples before and after enrichment, and the calculated fold increase.

Table SI.7: Endogenous content of the mtDNA present in the fixative samples before and after enrichment, and the calculated fold increase.

Table SI.8: Mitochondrial DNA haplogroup estimation after the hybridization capture, indicating the quality of the estimate and percentage of the contamination, and percentage of damage in the reads.

Table SI.9: Endogenous content of the pathogen DNA present in the tissue samples before and after enrichment, and the calculated fold increase.

Table SI.10: Endogenous content of the pathogen DNA present in the fixative samples before and after enrichment, and the calculated fold increase.

Figure SI.1: Richness of bacteria expressed with alpha diversity indices observed (top) and Shannon Index (bottom), both separated based on the type of fixative (EtOH70 in green, Kaiserling in blue) and negative controls (Blank in red).

Figure SI.2: Main 20 bacterial families present in the samples expressed in their percentage of abundance, separated by blank, liquid or tissue samples. EB = Extraction Blank; LB = Library Blank; Lon = London; E = Ethanol; LN = Lymph Node; T = Tissue; B = Bone; C = Cartilage; CS = Cross Section; M = Mucosa.