Biological Samples |
|
Ancient skeletal element |
This study |
I0308 |
Ancient skeletal element |
This study |
I0309 |
Ancient skeletal element |
This study |
I2230 |
Ancient skeletal element |
This study |
I2232 |
Ancient skeletal element |
This study |
I7086 |
Ancient skeletal element |
This study |
I7088 |
Ancient skeletal element |
This study |
I7090 |
Ancient skeletal element |
This study |
I1748 |
Ancient skeletal element |
This study |
I8348 |
Ancient skeletal element |
This study |
I8349 |
Ancient skeletal element |
This study |
I8350 |
Ancient skeletal element |
This study |
I3443 |
Ancient skeletal element |
This study |
I5456 |
Ancient skeletal element |
This study |
I5457 |
Ancient skeletal element |
This study |
I9054_d |
Ancient skeletal element |
This study |
I9055_d |
Ancient skeletal element |
This study |
I9056_d |
Ancient skeletal element |
This study |
I9057_d |
Ancient skeletal element |
This study |
I9058_d |
Ancient skeletal element |
This study |
CP18 |
Ancient skeletal element |
This study |
CP21 |
Ancient skeletal element |
This study |
CP22 |
Ancient skeletal element |
This study |
CP23 |
Ancient skeletal element |
This study |
CP25 |
Ancient skeletal element |
This study |
CP26 |
Ancient skeletal element |
This study |
CP19 |
Ancient skeletal element |
This study |
LAR001 |
Ancient skeletal element |
This study |
LAR002 |
Ancient skeletal element |
This study |
MOS001 |
Ancient skeletal element |
This study |
I1752 |
Ancient skeletal element |
This study |
I1754 |
Ancient skeletal element |
This study |
I1753 |
Ancient skeletal element |
This study |
I11974 |
Ancient skeletal element |
This study |
I2537 |
Ancient skeletal element |
This study |
CUN008 |
Ancient skeletal element |
This study |
CP8 |
Ancient skeletal element |
This study |
CP29 |
Ancient skeletal element |
This study |
I2261 |
Ancient skeletal element |
This study |
I0237 |
Ancient skeletal element |
This study |
I1357 |
Ancient skeletal element |
This study |
I1484 |
Ancient skeletal element |
This study |
I1485 |
Ancient skeletal element |
This study |
I1742 |
Ancient skeletal element |
This study |
I2551 |
Ancient skeletal element |
This study |
I0039 |
Ancient skeletal element |
This study |
I0040 |
Ancient skeletal element |
This study |
I0038 |
Ancient skeletal element |
This study |
I0041 |
Ancient skeletal element |
This study |
I0238 |
|
Chemicals, Peptides, and Recombinant Proteins |
|
Pfu Turbo Cx Hotstart DNA Polymerase |
Agilent Technologies |
Cat# 600412 |
Herculase II Fusion DNA Polymerase |
Agilent Technologies |
Cat# 600679 |
2x HI-RPM hybridization buffer |
Agilent Technologies |
Cat# 5190-0403 |
0.5 M EDTA pH 8.0 |
BioExpress |
Cat# E177 |
Sera-Mag Magnetic Speed-beads Carboxylate-Modified (1 μm, 3EDAC/PA5) |
GE LifeScience |
Cat# 65152105050250 |
USER enzyme |
New England Biolabs |
Cat# M5505 |
UGI |
New England Biolabs |
Cat# M0281 |
Bst DNA Polymerase2.0, large frag. |
New England Biolabs |
Cat# M0537 |
PE buffer concentrate |
QIAGEN |
Cat# 19065 |
Proteinase K |
Sigma Aldrich |
Cat# P6556 |
Guanidine hydrochloride |
Sigma Aldrich |
Cat# G3272 |
3M Sodium Acetate (pH 5.2) |
Sigma Aldrich |
Cat# S7899 |
Water |
Sigma Aldrich |
Cat# W4502 |
Tween-20 |
Sigma Aldrich |
Cat# P9416 |
Isopropanol |
Sigma Aldrich |
Cat# 650447 |
Ethanol |
Sigma Aldrich |
Cat# E7023 |
5M NaCl |
Sigma Aldrich |
Cat# S5150 |
1M NaOH |
Sigma Aldrich |
Cat# 71463 |
20% SDS |
Sigma Aldrich |
Cat# 5030 |
PEG-8000 |
Sigma Aldrich |
Cat# 89510 |
1 M Tris-HCl pH 8.0 |
Sigma Aldrich |
Cat# AM9856 |
dNTP Mix |
Thermo Fisher Scientific |
Cat# R1121 |
ATP |
Thermo Fisher Scientific |
Cat# R0441 |
10x Buffer Tango |
Thermo Fisher Scientific |
Cat# BY5 |
T4 Polynucleotide Kinase |
Thermo Fisher Scientific |
Cat# EK0032 |
T4 DNA Polymerase |
Thermo Fisher Scientific |
Cat# EP0062 |
T4 DNA Ligase |
Thermo Fisher Scientific |
Cat# EL0011 |
Maxima SYBR Green kit |
Thermo Fisher Scientific |
Cat# K0251 |
50x Denhardt’s solution |
Thermo Fisher Scientific |
Cat# 750018 |
SSC Buffer (20x) |
Thermo Fisher Scientific |
Cat# AM9770 |
GeneAmp 10x PCR Gold Buffer |
Thermo Fisher Scientific |
Cat# 4379874 |
Dynabeads MyOne Streptavidin T1 |
Thermo Fisher Scientific |
Cat# 65602 |
Salmon sperm DNA |
Thermo Fisher Scientific |
Cat# 15632-011 |
Human Cot-I DNA |
Thermo Fisher Scientific |
Cat# 15279011 |
DyNAmo HS SYBR Green qPCR Kit |
Thermo Fisher Scientific |
Cat# F410L |
Methanol, certified ACS |
VWR |
Cat# EM-MX0485-3 |
Acetone, certified ACS |
VWR |
Cat# BDH1101-4LP |
Dichloromethane, certified ACS |
VWR |
Cat# EMD-DX0835-3 |
Hydrochloric acid, 6N, 0.5N & 0.01N |
VWR |
Cat# EMD-HX0603-3 |
|
Critical Commercial Assays |
|
High Pure Extender from Viral Nucleic Acid Large Volume Kit |
Roche |
Cat# 5114403001 |
MinElute PCR Purification Kit |
QIAGEN |
Cat# 28006 |
NextSeq 500/550 High Output Kit v2 (150 cycles) |
Illumina |
Cat# FC-404-2002 |
HiSeq 4000 SBS Kit (50/75 cycles) |
Illumina |
Cat# FC-410-1001/2 |
|
Deposited Data |
|
Raw and analyzed data (European nucleotide archive) |
This study |
ENA: PRJEB28961 |
|
Software and Algorithms |
|
Samtools |
Li, 2011, Li et al., 2009
|
http://samtools.sourceforge.net/ |
BWA |
Li and Durbin, 2009 |
http://bio-bwa.sourceforge.net/ |
ADMIXTOOLS |
Patterson et al., 2012 |
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 |
AdapterRemoval v2 |
Schubert et al., 2016 |
https://github.com/MikkelSchubert/adapterremoval |
Dedup |
Peltzer et al., 2016 |
https://eager.readthedocs.io/en/latest/ |
smartpca |
Patterson et al., 2006 |
https://www.hsph.harvard.edu/alkes-price/software/ |
PMDtools |
Skoglund et al., 2014 |
https://github.com/pontussk/PMDtools |
Haplofind |
Vianello et al., 2013 |
https://haplofind.unibo.it |
Yfitter |
https://sourceforge.net/projects/yfitter/ |
https://sourceforge.net/projects/yfitter/ |
Schmutzi |
Renaud et al., 2015 |
https://grenaud.github.io/schmutzi/ |
ANGSD |
Korneliussen et al., 2014 |
https://github.com/ANGSD/angsd |
MEGA6 |
Tamura et al., 2013 |
https://www.megasoftware.net |
mapDamage2.0 |
Jónsson et al., 2013 |
https://ginolhac.github.io/mapDamage/ |