Svalbard 2010 mesocosm experiment: Protistan diversity
Hierarchical clustering. Taxonomic assignment of reads was performed using a preexisting database of SSU rDNA sequences from including XXX reference sequences generated by Sanger sequencing. Experimental amplicons (reads), sorted by abundance, were then concatenated with the reference extracted sequ...
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Online Access: | https://dx.doi.org/10.1594/pangaea.777733 https://doi.pangaea.de/10.1594/PANGAEA.777733 |
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ftdatacite:10.1594/pangaea.777733 2023-05-15T17:50:45+02:00 Svalbard 2010 mesocosm experiment: Protistan diversity De Vargas, Colomban Bittner, Lucie 2010 text/tab-separated-values https://dx.doi.org/10.1594/pangaea.777733 https://doi.pangaea.de/10.1594/PANGAEA.777733 en eng PANGAEA - Data Publisher for Earth & Environmental Science https://dx.doi.org/10.1594/pangaea.769833 Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 CC-BY Sample ID Experimental treatment Experiment day Fraction Sequence abundance Number of sequences Fraction of sample Kingdom Phylum Class Order Family Biological Impacts of Ocean Acidification BIOACID European Project on Ocean Acidification EPOCA Dataset dataset 2010 ftdatacite https://doi.org/10.1594/pangaea.777733 https://doi.org/10.1594/pangaea.769833 2022-02-09T13:12:06Z Hierarchical clustering. Taxonomic assignment of reads was performed using a preexisting database of SSU rDNA sequences from including XXX reference sequences generated by Sanger sequencing. Experimental amplicons (reads), sorted by abundance, were then concatenated with the reference extracted sequences sorted by decreasing length. All sequences, experimental and referential, were then clustered to 85% identity using the global alignment clustering option of the uclust module from the usearch v4.0 software (Edgar, 2010). Each 85% cluster was then reclustered at a higher stringency level (86%) and so on (87%, 88%,…) in a hierarchical manner up to 100% similarity. Each experimental sequence was then identified by the list of clusters to which it belonged at 85% to 100% levels. This information can be viewed as a matrix with the lines corresponding to different sequences and the columns corresponding to the cluster membership at each clustering level. Taxonomic assignment for a given read was performed by first looking if reference sequences clustered with the experimental sequence at the 100% clustering level. If this was the case, the last common taxonomic name of the reference sequence(s) within the cluster was used to assign the environmental read. If not, the same procedure was applied to clusters from 99% to 85% similarity if necessary, until a cluster was found containing both the experimental read and reference sequence(s), in which case sequences were taxonomically assigned as described above. Dataset Ocean acidification Svalbard DataCite Metadata Store (German National Library of Science and Technology) Svalbard |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
Sample ID Experimental treatment Experiment day Fraction Sequence abundance Number of sequences Fraction of sample Kingdom Phylum Class Order Family Biological Impacts of Ocean Acidification BIOACID European Project on Ocean Acidification EPOCA |
spellingShingle |
Sample ID Experimental treatment Experiment day Fraction Sequence abundance Number of sequences Fraction of sample Kingdom Phylum Class Order Family Biological Impacts of Ocean Acidification BIOACID European Project on Ocean Acidification EPOCA De Vargas, Colomban Bittner, Lucie Svalbard 2010 mesocosm experiment: Protistan diversity |
topic_facet |
Sample ID Experimental treatment Experiment day Fraction Sequence abundance Number of sequences Fraction of sample Kingdom Phylum Class Order Family Biological Impacts of Ocean Acidification BIOACID European Project on Ocean Acidification EPOCA |
description |
Hierarchical clustering. Taxonomic assignment of reads was performed using a preexisting database of SSU rDNA sequences from including XXX reference sequences generated by Sanger sequencing. Experimental amplicons (reads), sorted by abundance, were then concatenated with the reference extracted sequences sorted by decreasing length. All sequences, experimental and referential, were then clustered to 85% identity using the global alignment clustering option of the uclust module from the usearch v4.0 software (Edgar, 2010). Each 85% cluster was then reclustered at a higher stringency level (86%) and so on (87%, 88%,…) in a hierarchical manner up to 100% similarity. Each experimental sequence was then identified by the list of clusters to which it belonged at 85% to 100% levels. This information can be viewed as a matrix with the lines corresponding to different sequences and the columns corresponding to the cluster membership at each clustering level. Taxonomic assignment for a given read was performed by first looking if reference sequences clustered with the experimental sequence at the 100% clustering level. If this was the case, the last common taxonomic name of the reference sequence(s) within the cluster was used to assign the environmental read. If not, the same procedure was applied to clusters from 99% to 85% similarity if necessary, until a cluster was found containing both the experimental read and reference sequence(s), in which case sequences were taxonomically assigned as described above. |
format |
Dataset |
author |
De Vargas, Colomban Bittner, Lucie |
author_facet |
De Vargas, Colomban Bittner, Lucie |
author_sort |
De Vargas, Colomban |
title |
Svalbard 2010 mesocosm experiment: Protistan diversity |
title_short |
Svalbard 2010 mesocosm experiment: Protistan diversity |
title_full |
Svalbard 2010 mesocosm experiment: Protistan diversity |
title_fullStr |
Svalbard 2010 mesocosm experiment: Protistan diversity |
title_full_unstemmed |
Svalbard 2010 mesocosm experiment: Protistan diversity |
title_sort |
svalbard 2010 mesocosm experiment: protistan diversity |
publisher |
PANGAEA - Data Publisher for Earth & Environmental Science |
publishDate |
2010 |
url |
https://dx.doi.org/10.1594/pangaea.777733 https://doi.pangaea.de/10.1594/PANGAEA.777733 |
geographic |
Svalbard |
geographic_facet |
Svalbard |
genre |
Ocean acidification Svalbard |
genre_facet |
Ocean acidification Svalbard |
op_relation |
https://dx.doi.org/10.1594/pangaea.769833 |
op_rights |
Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1594/pangaea.777733 https://doi.org/10.1594/pangaea.769833 |
_version_ |
1766157629304864768 |