Supplementary information from: An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used, including the skeletons’ historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological..., This dataset includes FastQC reports for raw data (Supplementary Material 1), FastQC reports for trimmed data (Supplementary Material 2), Fastp reports on the impact of data quality filtering (Supplementary Material 3), and mapDamage plots of the human DNA sequences recovered from the datasets (Supplementary Material 4).
Detailed methods may be found in the associated publication. The dataset was collected from archaeological dental calculus and associated bone samples. DNA was extracted within dedicated biomolecular clean labs. After crushing to a powder, samples were pre-digested for 5 minutes with 1 mL of 0.5M EDTA to remove possible surface contamination. This pre-digestion supernatant was removed, and a further 1.1 mL of 0.5M EDTA was added and rotated at room temperature for seven days to fully demineralize. For the majority of samples, DNA was extracted from the dental calculus and bone samples using a protocol based on Dabney et al. (2013). All DNA extracts were quantified via Q..., , # Supplementary information from: An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

[https://doi.org/10.5061/dryad.jdfn2z3mk](https://doi.org/10.5061/dryad.jdfn2z3mk)

## Description of the data and file structure

Quality and authentication reports for metagenomic sequencing data associated with ancient dental calculus samples and associated controls. These include 174 samples (348 fastq files using paired end reads) from modern (n=10) and archaeological dental calculus (n=133) and tooth (n=2) samples, environmental controls (bone; n=7), and laboratory controls (extraction and library blanks; n=22).

### Files and variables

#### File: Supplementary_Material_3_Fastp_reports_raw.zip

**Description:** Results of Fastp analysis for metagenomic data obtained from ancient dental calculus, and associated bone and blank controls. The zip folder contains 174 html files with the Fastp report for each sample - the file name of be...,

考古牙石（Archaeological dental calculus）可深入揭示古代人类口腔微生物组（oral microbiome）。本数据集为多时期、多站点的古代霰弹枪宏基因组（shotgun metagenomic）数据集，共包含174份样本，主要取自英国各骨骼馆藏的考古牙石。本文详述了所用全部材料，包括骨骼样本的历史时期、埋藏地点、生物学性别及年龄鉴定结果，数据可访问性，以及与环境和实验对照相关的额外细节。此外，本文还介绍了数据集构建所涉及的实验与生物信息学方法，并在质量评估、损伤评估及去污流程之后，讨论了数据的技术有效性。我们在宏基因组分析前完成生物考古学元数据（metadata）的收集、开放共享与评估的工作，旨在进一步推动考古领域相关探索……本数据集包含原始数据的FastQC报告（补充材料1）、修剪后数据的FastQC报告（补充材料2）、数据质量过滤效果的Fastp报告（补充材料3），以及从本数据集中获取到的人类DNA序列的mapDamage绘图结果（补充材料4）。详细方法可参见相关发表文献。本数据集采集自考古牙石及配套骨样本。DNA提取工作在专用生物分子洁净实验室中完成。样本经粉碎为粉末后，先用1mL 0.5M乙二胺四乙酸（EDTA）预消化5分钟以去除可能的表面污染。移除该预消化上清液后，再加入1.1mL 0.5M EDTA，于室温下旋转孵育7天以完成完全脱矿。对于绝大多数样本，我们采用基于Dabney等人（2013）的方案，从牙石及骨样本中提取DNA。所有DNA提取物均通过Q...进行定量。
# 补充信息来源：一项跨越5000年的大型考古牙石数据集，用于古代人类口腔微生物组研究
https://doi.org/10.5061/dryad.jdfn2z3mk

## 数据与文件结构说明
与古代牙石样本及配套对照样本的宏基因组测序数据相关的质量与验证报告。其中包含174份样本：现代样本（n=10）、考古牙石样本（n=133）、牙齿样本（n=2）、环境对照样本（骨；n=7），以及实验对照样本（提取与建库空白；n=22），对应348个双端测序fastq文件。

### 文件与变量
#### 文件：Supplementary_Material_3_Fastp_reports_raw.zip
**描述：** 来自古代牙石、配套骨样本及空白对照的宏基因组数据的Fastp分析结果。该压缩包包含174份HTML文件，对应每份样本的Fastp报告——文件名原文此处截断。