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Data released on June 27, 2017

Supporting data for "Comparative performance of the BGISEQ-500 vs Illumina sequencing platforms for palaeogenomic sequencing"

Bocherens, H; Caroe, C; Fedorov, S; Fu, S; Geng, C; Germonpré, M; Gopalakrishnan, S; K Kuderna, L, F; Liu, S; Marques-Bonet, T; Petersen, B; Sicheritz-Ponten, T; Sinding, M, S; Tze Mak, S, S; Vieira, F, G; Zhang, G; Zhang, W; Gilbert, M, P; Jiang, H (2017): Supporting data for "Comparative performance of the BGISEQ-500 vs Illumina sequencing platforms for palaeogenomic sequencing" GigaScience Database. http://dx.doi.org/10.5524/100303 RIS BibTeX Text

Ancient DNA research has been revolutionised following development of ‘Next Generation’ Sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples.
The data generated was largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (p=0.371) and average sequence length (p=0718) of endogenous nuclear DNA, sequence GC content (p=0.311), double stranded DNA damage rate (p=0.309), and sequence clonality (p=0.093). Small significant differences were found in single strand DNA damage rate (δS, slight lower for the BGISEQ-500, p=0.011) and the background rate of difference from the reference genome (θ, slightly higher for BGISEQ-500, p=0.012). This may result from the differences in amplification cycles used to PCR amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (p=0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA.
Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix049

Additional information:

http://www.erda.dk/public/archives/YXJjaGl2ZS1zajh4ZTQ=/published-archive.html

Protocols.io:

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Accessions (data included in GigaDB):

ENA: PRJEB21089

Keywords:

ancient DNA BGISEQ-500 Illumina HiSeq 2500 comparative performance 

Genomic

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Funding:

  • Funding body - ERC Consolidator Grant
  • Award ID - 681396
  • Comment - Extinction Genomics
  • Awardee - MTP Gilbert
  • Funding body - Marie Skłodowska-Curie Actions
  • Award ID - H2020-MSCA-ETN-643063
  • Comment - Microwine
  • Awardee - MTP Gilbert
  • Funding body - Danish Council for Independent Research
  • Award ID - 4005-00107
  • Comment - Wine-ometrics
  • Awardee - MTP Gilbert
  • Funding body - Ministerio de Economía y Competitividad
  • Award ID - BFU2014-55090-P
  • Comment - FPI fellowship
  • Awardee - LFK Kuderna
  • Funding body - Ministerio de Economía y Competitividad
  • Award ID - BFU2015-6215-ERC
  • Comment - U01 MH106874
  • Awardee - T Marques-Bonet
  • Funding body - Ministerio de Economía y Competitividad
  • Award ID - BFU2014-55090-P
  • Comment - MENCO
  • Awardee - T Marques-Bonet
  • Funding body - Marie Skłodowska-Curie Actions
  • Award ID - H2020-MSCA-IF-2014
  • Comment - 655732 Wherewolf
  • Awardee - S Gopalakrishnan

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
CN19219612grey wolfgray wolfCanis lupus Description:DNA extracted from historic wolf hide
Alternative names:CN 1921
Environment (material):Hide
...
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CN2149612grey wolfgray wolfCanis lupus Description:DNA extracted from historic wolf hide
Alternative names:CN 214
Environment (material):Hide
...
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FRC9612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:FRC
Environment (material):Cartilage
...
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L9612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:L
Environment (material):Liver
...
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M19612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:M1
Environment (material):Muscle
...
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MGUH_VP_33329612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:P84
Environment (material):Humerus
...
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NKA_1950x29069615dogsdogCanis lupus familiaris Description:DNA extracted from archaeological dog ...
Alternative names:P83
Environment (material):Canine tooth
...
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ZMK_350/19829615dogsdogCanis lupus familiaris Description:DNA extracted from archaeological dog ...
Alternative names:P79
Environment (material):Tibia
...
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Displaying 1-8 of 8 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
CN1921Tabular DataTEXT0.58 KB2017-06-20
CN1921Tabular DataTEXT0.58 KB2017-06-20
CN1921Tabular DataUNKNOWN49.04 KB2017-06-20
CN1921Tabular DataTEXT0.3 KB2017-06-20
CN1921OtherUNKNOWN25.07 KB2017-06-20
CN1921Tabular DataTEXT495.98 KB2017-06-20
CN1921Tabular DataTEXT1.42 KB2017-06-20
CN1921Tabular DataTEXT24.04 KB2017-06-20
CN1921Tabular DataUNKNOWN6.65 KB2017-06-20
CN1921TextUNKNOWN7.32 KB2017-06-20
Displaying 1-10 of 216 File(s).

History:

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