Open access bench protocols
Numerous protocols have been published for the study of ancient biomolecules, but few provide step-by-step instructions, making many difficult to implement in practice. Below are open access bench protocols published in accordance with open science principles in order to make each step of the protocol explicit and reproducible. If you have add additional resources to suggest, please send your suggestions to webmaster@isbarch.org.
Ancient DNA
A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing V.2: a collection of open-access bench protocols for the extraction and preparaton of ancient DNA (aDNA) for Illumina high throughput sequencing. All protocols have been adapted after published protocols (see each for the corresponding original publication), and are used primarily in the Department of Archaeogenetics at the MPI-EVA (Leipzig, Germany). Protocols in the collection include:
- Minimally-invasive sampling of pars petrosa (os temporale) for ancient DNA extraction (adapted from Pinhasi et al. 2015)
- Tooth sampling from the inner pulp chamber for ancient DNA extraction
- Dental calculus field sampling protocol (Sabin protocol)
- Dental calculus field sampling protocol (adapted from Velsko and Warinner 2017)
- Ancient DNA extraction from skeletal material (adapted from Dabney et al. 2013)
- Ancient DNA extraction from dental calculus (adapted from Mann et al. 2018)
- Library adapter preparation for dual-index double stranded DNA sequencing (adapted from Meyer and Kircher 2010)
- Non-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing (adapted from Meyer and Kircher 2010)
- Half-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing (adapted from Rohland et al. 2015 and Meyer and Kircher 2010)
- Full-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing (adapted from Briggs et al. 2010 and Meyer and Kircher 2010)
- Illumina double-stranded DNA dual indexing for ancient DNA (adapted from Kircher et al. 2012)
- DNA library amplification and pooling for Illumina sequencing
Proteomics
Zooarchaeology by Mass Spectrometry (ZooMS) Pretreatment protocols for bone material: a collection of established ZooMS protocols for bone
- ZooMS for bone material - AmBiC protocol
- ZooMS for bone material - Acid incoluble protocol
- ZooMS for boen material - Acid soluble protocol
Identifying ZooMS Spectra (mammals) using mMass: a guide to identifying ZooMS spectra for mammals using the open-source program mMass (Niedermeyer and Strohalm 2012). This guide is intended as a learning tool for students and researchers at the University of Tubingen and is not meant to replace formal ZooMS marker training.
Ancient Proteins Extraction Protocol: a FASP-based protocol for ancient protein recovery for LC-MS/MS analysis