Deliverables
NEOGENE Data Management Plan: The project involves production of human and sheep ancient DNA data (generated by whole genome shotgun sequencing and genotyping) and radiocarbon data. It also includes compiling genetic data and archaeological material culture data from literature surveys and correspondence with research teams. We will ensure that the data remains findable, accessible, interoperable and re-usable in the following ways: - All mapped genome sequencing data (in .bam format) will be made available through the European Nucleotide Archive (https://www.ebi.ac.uk/ena), following the current standard procedure in the archaeogenomics field; - All processed genome datasets (in PLINK flat files format, .map and .ped) and radiocarbon dating results of the biological samples will be available through our local web server at METU; - All raw material culture datasets (in spreadsheet format) will be available through our local web server at METU; - All computer code used in the analyses will be shared through GitHub (github.com), and also through our local web server at METU; - All raw sequencing data (in .fastq format) will be available upon request, following the current standard procedure in the aDNA field (raw aDNA shotgun sequencing reads are usually not submitted to databases as the majority of reads represent microbial contamination, thus hindering data reuse); - All raw sequencing data and radiocarbon dating results will be stored in two physically separate servers at METU for ensuring data safety; - All analysis results will be published in open access journals or choosing the open access option. We will further encourage all archaeology and anthropology teams working with us to openly share their data through “Open Context” (www.opencontext.org; a subproject of Alexandria Archive Institute) and through Digital Archaeology Record (www.tdar.org).
Publications
Author(s):
Erinç Yurtman, Onur Özer, Eren Yüncü, Nihan Dilşad Dağtaş, Dilek Koptekin, Yasin Gökhan Çakan, Mustafa Özkan, Ali Akbaba, Damla Kaptan, Gözde Atağ, Kıvılcım Başak Vural, Can Yümni Gündem, Louise Martin, Gülşah Merve Kılınç, Ayshin Ghalichi, Sinan Can Açan, Reyhan Yaka, Ekin Sağlıcan, Vendela Kempe Lagerholm, Maja Krzewińska, Torsten Günther, Pedro Morell Miranda, Evange
Published in:
Communications Biology volume, Issue 4, Article number: 1279 (2021), 2021, ISSN 2399-3642
Publisher:
NATURE
DOI:
10.1038/s42003-021-02794-8
Author(s):
Murat Karakoç; Hasan Can Gemici; Murat Dirican; Okşan Başoğlu; Çiğdem Atakuman
Published in:
Documenta Praehistorica, Vol 50 (2023), Issue 4, 2023, ISSN 1854-2492
Publisher:
Ljubljana: Založba Univerze v Ljubljani
DOI:
10.4312/dp.50.5
Author(s):
Dilek Koptekin, Eren Yüncü, Ricardo Rodríguez-Varela, N. Ezgi Altınışık, Nikolaos Psonis,Natalia Kashuba, Sevgi Yorulmaz, Robert George, Duygu Deniz Kazancı, Damla Kaptan, Kanat Gürün, Kıvılcım Başak Vural, Hasan Can Gemici, Despoina Vassou, Evangelia Daskalaki, Cansu Karamurat, Vendela K. Lagerholm, Ömür Dilek Erdal, Emrah Kırdök, Aurelio Marangoni, Andreas Schachner, Handan Üs
Published in:
Current Biology, Issue Volume 33, Issue 1, 9 January 2023,, 2022, Page(s) Pages 41-57.e15, ISSN 1879-0445
Publisher:
Science Direct
DOI:
10.1016/j.cub.2022.11.034
Author(s):
N. Ezgi Altınışık; Duygu Deniz Kazancı; Ayça Aydoğan; Hasan Can Gemici; Ömür Dilek Erdal; Savaş Sarıaltun; Kıvılcım Başak Vural; Dilek Koptekin; Kanat Gürün; Ekin Sağlıcan; Daniel Fernandes; Gökhan Çakan; Meliha Melis Koruyucu; Vendela Kempe Lagerholm; Cansu Karamurat; Mustafa Özkan; Gülşah Merve Kılınç; Arda Sevkar; Elif Sürer; Anders Götherström; Çiğdem Atakuman;
Published in:
Science Advances, Issue 7, 2022, ISSN 2375-2548
Publisher:
Science Advances
DOI:
10.1126/sciadv.abo3609
Author(s):
Ceballos, Francisco C.; Gürün, Kanat; Altınışık, N. Ezgi; Gemici, Hasan Can; Karamurat, Cansu; Koptekin, Dilek; Vural, Kıvılcım Başak; Mapelli, Igor; Sağlıcan, Ekin; Sürer, Elif; Erdal, Yılmaz Selim; Götherström, Anders; Özer, Füsun; Atakuman, Çiğdem; Somel, Mehmet
Published in:
CURRENT BIOLOGY, Issue 2, 2021, Page(s) P3925-3934.e8, ISSN 1097-4172
Publisher:
CELL PRESS
DOI:
10.1016/j.cub.2021.06.027
Author(s):
Mustafa Özkan; Kanat Gürün; Eren Yüncü; Kıvılcım Başak Vural; Gözde Atağ; Ali Akbaba; Fatma Rabia Fidan; Ekin Sağlıcan; N. Ezgi Altınışık; Dilek Koptekin; Kamilla Pawłowska; Ian Hodder; Sarah E. Adcock; Benjamin S. Arbuckle; Sharon R. Steadman; Gregory McMahon; Yılmaz Selim Erdal; C. Can Bilgin; Eva-Maria Geigl; Anders Götherstrom; Thierry Grange; İnci Togan; Füsun Özer; Meh
Published in:
Molecular Ecology- Biorvix, Issue 7, 2023, ISSN 0962-1083
Publisher:
Blackwell Publishing Inc.
DOI:
10.1101/2023.06.05.543765
Author(s):
Gözde Atağ; Kıvılcım Başak Vural; Damla Kaptan; Mustafa Özkan; Dilek Koptekin; Ekin Sağlıcan; Sevcan Doğramacı; Mevlüt Köz; Ardan Yılmaz; Arda Söylev; İnci Togan; Mehmet Somel; Füsun Özer
Published in:
Open Research Europe, Issue 5, 2022, ISSN 2732-5121
Publisher:
Open research Europe
DOI:
10.1101/2022.06.06.491147
Author(s):
Arda Söylev; Sevim Seda Çokoglu; Dilek Koptekin; Can Alkan; Mehmet Somel
Published in:
Crossref, Issue 1, 2022, ISSN 1553-7358
Publisher:
PLOS COMPUTATIONAL BIOLOGY
DOI:
10.1101/2021.12.17.473150
Author(s):
Gözde Atağ, Damla Kaptan, Eren Yüncü, Kıvılcım Başak Vural, Paolo Mereu, Monica Pirastru, Mario Barbato, Giovanni Giuseppe Leoni, Merve Nur Güler, Tuğçe Er, Elifnaz Eker, Tunca Deniz Yazıcı, Muhammed Sıddık Kılıç, Nefize Ezgi Altınışık, Ecem Ayşe Çelik, Pedro Morell Miranda, Marianne Dehasque, Viviana Floridia, Anders Götherström, Cemal Can Bilgin, İnci Togan, Tors
Published in:
Genome Biology and Evolution, Issue Volume 16, Issue 5, 2024, ISSN 1759-6653
Publisher:
Oxford University Press
DOI:
10.1093/gbe/evae090
Author(s):
Reyhan Yaka; Maja Krzewińska; Vendela Kempe Lagerholm; Anna Linderholm; Füsun Özer; Mehmet Somel & Anders Götherström
Published in:
Biotechniques, Issue Volume 76, 2024 - Issue 5: BioTechniques, 2023, ISSN 1940-9818
Publisher:
Future Science Ltd
DOI:
10.2144/btn-2023-0107
Author(s):
Reyhan Yaka
Published in:
2020
Publisher:
METU
Author(s):
Schotsmans, E M J; Busacca, G; Lin, S C; Vasi��, M; Lingle, A M; Veropoulidou, R; Mazzucato, C; Tibbetts, B; Haddow, S D; Somel, M; Toksoy-K��ksal, F; Kn��sel, C J; Milella, M
Published in:
NATURE-Scientific Reports, Issue 7, 2022, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-022-07284-3
Author(s):
Yaka R., Doğu A., Kaptan D., Dağtaş N. D. , Chyleński M., Vural K. B. , Altınışık N. E. , Mapelli I., Koptekin D., Karamurat C., Gemici H. C. , Yorulmaz S., Lagerholm V. K. , Fer E., Işıldak U., Ghalichi A., Kılınç G. M. , Mazzucato C., Juras A., Marciniak A., Larsen C. S. , Pilloud M., Haddow S. D. , Knüsel C. J. , Togan İ., Götherström A., Erdal Y. S. , Sürer E. , Özer F., Ata
Published in:
Peopling the Landscape of Çatalhöyük, 2021, Page(s) 395-405
Publisher:
The British Institute of Archaeology at Ankara
Searching for OpenAIRE data...
There was an error trying to search data from OpenAIRE
No results available