Study of infectious diseases in archaeological bone material – A dataset

Bones of human and ground sloth remains were analyzed for presence of Trypanosoma cruzi by conventional PCR using primers TC, TC1 and TC2. Sequence results amplified a fragment with the same product size as the primers (300 and 350pb). Amplified PCR product was sequenced and analyzed on GenBank, using Blast. Although these sequences did not match with these parasites they showed high amplification with species of bacteria. This article presents the methodology used and the alignment of the sequences. The display of this dataset will allow further analysis of our results and discussion presented in the manuscript “Finding the unexpected: a critical view on molecular diagnosis of infectious diseases in archaeological samples” (Pucu et al. 2017) [1].

Bones of human and ground sloth remains were analyzed for presence of Trypanosoma cruzi by conventional PCR using primers TC, TC1 and TC2. Sequence results amplified a fragment with the same product size as the primers (300 and 350pb). Amplified PCR product was sequenced and analyzed on GenBank, using Blast. Although these sequences did not match with these parasites they showed high amplification with species of bacteria. This article presents the methodology used and the alignment of the sequences. The display of this dataset will allow further analysis of our results and discussion presented in the manuscript "Finding the unexpected: a critical view on molecular diagnosis of infectious diseases in archaeological samples" (Pucu et  Value of the data Data will be useful to investigate differences in DNA sequence results This data allows the comparison with samples of similar archeological context. Data can be used to investigate methodologies and primers' design.

Data
We present data from bones of human remains from Brazil: Justino site, Sergipe (n ¼7), dated from 4380-3200 BP (Before Present); and Funerary Site São Gonçalo Garcia Church, Rio de Janeiro (n ¼7) dated from the end of the 18th century [1]. Some (n ¼5) bone fragments were also analyzed from an individual extinct giant ground sloth of the genus Eremotherium spp., from Lagoa dos Porcos site, Piauí, Brazil dated from 30.000 BC (Before Christ) [1]. Data include methodologies, primers' information and conditions (Table 1) and sequence alignment. (Figs. 1-3).

Pre-treatment and DNA extraction
Prior to DNA extraction, we macerated bone samples with a mortar and pestle in liquid nitrogen. Samples were re-suspended in a small amount of nuclease-free water for the sample to acquire adequate consistency for manipulation. The solution was incubated at 37°C for 30 mi. This step was followed by DNA extraction using PureLink s Genomic DNA Kit (Invitrogen), according to the tissue sample protocol. We followed manufacturer's instructions, with the following modifications: samples were incubated with digestion buffers proteinase K and RNAse for 2hs and the DNA was eluted in a final volume of 50 mL, previously incubated at room temperature for 3 min and centrifuged for 2 minutes.

Amplification of products
We conducted a reconstructive PCR on the samples, as the DNA was fragmented and this is recommended to increase amplification product. This step does not add primers in the mix. Protocol After this step, PCR was conducted with amplification products of the reconstructive PCR and also with purified DNA. We conducted the protocol described by Fernandes et al. [3], with the following conditions:      [4]. The authors amplified a part of the intergenic region of Trypanosoma cruzi mini-exon genes using a pool of oligonucleotides (see Table 1 for primers sequences and fragment sizes). These DNA markers define two phylogenetic lineages of Trypanosonoma cruzi (TC1 and TC2).

Sequencing and analysis
Amplified products were purified with Kit Wizard s SV Gel and PCR Clean-Up System (Promega), following manufacturers' protocols. Obtained products were sequenced directly in both strips in an automatic sequencer (Applied Biosystems) by platform UFF/Instituto Biomédico. The softwares Chromas Lite 2.1 and BioEdit 7.2.5 were used to edit, analyze, and align sequences, which were compared to the Genbank database.