Choose a pipeline:

From Human molar, Luxembourg Loschbour, sample Tooth (molar) Loschbour

Extracted: using 80 mg of tooth powder (http://dx.doi.org/10.1038/nprot.2007.247)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Harvard Medical School Biopolymers Facility, Boston
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
BWA/bam-rmdup2/GATK/ samtools version 0.5.10/0.4.9/1.3-25/0.1.18
Aligned to:
hg19
Average fold coverage:
7.200x

From Human skull, Germany ACAD8240, sample Calculus (LBK_Kit) LBK1

Extracted 2012-10-01: Decontamination method came from: doi:10.1038/ncomms2656 (http://dx.doi.org/10.1038/ng.2536)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Max Planck Institute for Developmental Biology , Tübingen
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
BWA/bam-rmdup2/GATK/ samtools version 0.5.10/0.4.9/1.3-25/0.1.18
Aligned to:
hg19
Average fold coverage:
19.100x

From Human skeleton, Sweden I0011, sample Tooth (Motala1) Motala1

Extracted: (http://dx.doi.org/10.1038/nature13673)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Illumina, San Diego
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
SeqPrep/BWA/samtools version xx/0.5.10/0.1.18
Aligned to:
hg19
Average fold coverage:
0.180x

From Human skeleton, Sweden I0012, sample Tooth (Motala2) Motala2

Extracted: using 100 mg (http://dx.doi.org/10.1002/(SICI)1096-8644(199804)105:4<539::AID-AJPA10>3.0.CO;2-1)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Illumina, San Diego
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
SeqPrep/BWA/samtools version xx/0.5.10/0.1.18
Aligned to:
hg19
Average fold coverage:
0.150x

From Human skeleton, Sweden I0013, sample Tooth (Motala3) Motala3

Extracted: (http://dx.doi.org/10.1038/nature13673)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Illumina, San Diego
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
SeqPrep/BWA/samtools version xx/0.5.10/0.1.18
Aligned to:
hg19
Average fold coverage:
0.550x

From Human skeleton, Sweden I0014, sample Tooth (Motala4) Motala4

Extracted: (http://dx.doi.org/10.1038/nature13673)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Illumina, San Diego
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
SeqPrep/BWA/samtools version xx/0.5.10/0.1.18
Aligned to:
hg19
Average fold coverage:
0.070x

From Human skeleton, Sweden I0015, sample Tooth (Motala6) Motala6

Extracted: using 100 mg (http://dx.doi.org/10.1002/(SICI)1096-8644(199804)105:4<539::AID-AJPA10>3.0.CO;2-1)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Illumina, San Diego
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
SeqPrep/BWA/samtools version xx/0.5.10/0.1.18
Aligned to:
hg19
Average fold coverage:
0.024x

From Human skeleton, Sweden I0016, sample Tooth (Motala9) Motala9

Extracted: (http://dx.doi.org/10.1038/nature13673)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Illumina, San Diego
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
SeqPrep/BWA/samtools version xx/0.5.10/0.1.18
Aligned to:
hg19
Average fold coverage:
0.010x

From Human skeleton, Sweden I0017, sample Tooth (Motala12) Motala12

Extracted: using 100 mg (http://dx.doi.org/10.1002/(SICI)1096-8644(199804)105:4<539::AID-AJPA10>3.0.CO;2-1)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/ 10.1093/nar/gkp1163)
Repair method:
uracil DNA glycosylase (UDG) and endonuclease VIII (endo VIII) treatment
Enrichment method:
PCR

Sequence

Sequenced at:
Illumina, San Diego
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq 2000 (chemistry version 3)
Sequencing options:
default
Output format:
fastq
Quality scale:
33

Processing

Processed using:
SeqPrep/BWA/samtools version xx/0.5.10/0.1.18
Aligned to:
hg19
Average fold coverage:
2.400x

Analysis

Analysed using samtools/bcftools version 1.2/1.2

Please cite as

Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H; Schraiber, Joshua G; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M; Brisighelli, Francesca; Busby, George BJ; Cali, Francesco; Churnosov, Mikhail; Cole, David EC; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A; Gallego Romero, Irene; Gubina, Marina; Hammer, Michael; Henn, Brenna M; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl A; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G; Ruiz-Linares, Andres; Tishkoff, Sarah A; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes (2014): Lazaridis_EuropePopulations. Online Ancient Genome Repository. Dataset. http://dx.doi.org/10.4225/55/578191DABEC93

Other Studies

This dataset doesn't appear in any other studies.

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