| Biological Samples |
| Ancient human skeletal elements |
This study |
See Table 1
|
| Chemicals, Peptides, and Recombinant Proteins |
| Pfu Turbo Cx Hotstart DNA Polymerase |
Agilent Technologies |
600412 |
| Herculase II Fusion DNA Polymerase |
Agilent Technologies |
600679 |
| 2x HI-RPM hybridization buffer |
Agilent Technologies |
5190–0403 |
| 0.5 M EDTA pH 8.0 |
BioExpress |
E177 |
| Silica magnetic beads |
G-Biosciences |
786–915 |
| Sera-Mag™ Magnetic Speed-beads™ Carboxylate-Modified (1μm, 3EDAC/PA5) |
GE LifeScience |
65152105050250 |
| USER enzyme |
New England Biolabs |
M5505 |
| UGI |
New England Biolabs |
M0281 |
| Bst DNA Polymerase2.0, large frag. |
New England Biolabs |
M0537 |
| PE buffer concentrate |
Qiagen |
19065 |
| Proteinase K |
Sigma Aldrich |
P6556 |
| Guanidine hydrochloride |
Sigma Aldrich |
G3272 |
| 3M Sodium Acetate (pH 5.2) |
Sigma Aldrich |
S7899 |
| Water |
Sigma Aldrich |
W4502 |
| Tween-20 |
Sigma Aldrich |
P9416 |
| Isopropanol |
Sigma Aldrich |
650447 |
| Ethanol |
Sigma Aldrich |
E7023 |
| 5M NaCl |
Sigma Aldrich |
S5150 |
| 1M NaOH |
Sigma Aldrich |
71463 |
| 20% SDS |
Sigma Aldrich |
5030 |
| PEG-8000 |
Sigma Aldrich |
89510 |
| 1 M Tris-HCl pH 8.0 |
Sigma Aldrich |
AM9856 |
| dNTP Mix |
Thermo Fisher Scientific |
R1121 |
| ATP |
Thermo Fisher Scientific |
R0441 |
| 10x Buffer Tango |
Thermo Fisher Scientific |
BY5 |
| T4 Polynucleotide Kinase |
Thermo Fisher Scientific |
EK0032 |
| T4 DNA Polymerase |
Thermo Fisher Scientific |
EP0062 |
| T4 DNA Ligase |
Thermo Fisher Scientific |
EL0011 |
| Maxima SYBR Green kit |
Thermo Fisher Scientific |
K0251 |
| 50x Denhardt’s solution |
Thermo Fisher Scientific |
750018 |
| SSC Buffer (20x) |
Thermo Fisher Scientific |
AM9770 |
| GeneAmp 10x PCR Gold Buffer |
Thermo Fisher Scientific |
4379874 |
| Dynabeads MyOne Streptavidin T1 |
Thermo Fisher Scientific |
65602 |
| Salmon sperm DNA |
Thermo Fisher Scientific |
15632–011 |
| Human Cot-I DNA |
Thermo Fisher Scientific |
15279011 |
| DyNAmo HS SYBR Green qPCR Kit |
Thermo Fisher Scientific |
F410L |
| Methanol, certified ACS |
VWR |
EM-MX0485–3 |
| Acetone, certified ACS |
VWR |
BDH1101–4LP |
| Dichloromethane, certified ACS |
VWR |
EMD-DX0835–3 |
| Hydrochloric acid, 6N, 0.5N & 0.01N |
VWR |
EMD-HX0603–3 |
| Critical Commercial Assays |
| High Pure Extender from Viral Nucleic Acid Large Volume Kit |
Roche |
5114403001 |
| NextSeq® 500/550 High Output Kit v2 (150 cycles) |
Illumina |
FC-404–2002 |
| Deposited Data |
| Raw and analyzed data |
This paper |
ENA: PRJEB40109 |
| Software and Algorithms |
| In-house bioinformatics tools |
https://github.com/DReichLab/ADNA-Tools |
https://github.com/DReichLab/ADNA-Tools |
| In-house data workflow |
https://github.com/DReichLab/adna-workflow |
https://github.com/DReichLab/adna-workflow |
| Samtools |
[68] |
http://samtools.sourceforge.net/ |
| BWA |
[54] |
http://bio-bwa.sourceforge.net/ |
| Picard |
https://broadinstitute.github.io/picard/ |
https://broadinstitute.github.io/picard/ |
| ADMIXTOOLS |
[67] |
https://github.com/DReichLab/AdmixTools |
| SeqPrep |
https://github.com/jstjohn/SeqPrep |
https://github.com/jstjohn/SeqPrep |
| bamrmdup |
https://bitbucket.org/ustenzel/biohazard |
https://bitbucket.org/ustenzel/biohazard |
| smartpca |
[65] |
https://www.hsph.harvard.edu/alkes-price/software/ |
| PMDtools |
[69] |
https://github.com/pontussk/PMDtools |
| Haplogrep 2 |
[56] |
http://haplogrep.uibk.ac.at/ |
| htsbox |
https://github.com/lh3/htsbox |
https://github.com/lh3/htsbox |
| contamMix |
[57] |
contact Philip Johnson plfj@umd.edu
|
| ANGSD |
[58] |
https://github.com/ANGSD/angsd |
| OxCal |
[59] |
https://c14.arch.ox.ac.uk/oxcal.html |
| MALDER |
[21] |
https://github.com/joepickrell/malder/tree/master/MALDER |
| DATES |
[22] |
https://github.com/priyamoorjani/DATES |
