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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ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.777733 2023-05-15T17:50:42+02:00 Svalbard 2010 mesocosm experiment: Protistan diversity De Vargas, Colomban Bittner, Lucie 2010-03-15 text/tab-separated-values, 93578 data points https://doi.pangaea.de/10.1594/PANGAEA.777733 https://doi.org/10.1594/PANGAEA.777733 en eng PANGAEA https://doi.org/10.1594/PANGAEA.769833 https://doi.pangaea.de/10.1594/PANGAEA.777733 https://doi.org/10.1594/PANGAEA.777733 CC-BY-3.0: Creative Commons Attribution 3.0 Unported Access constraints: unrestricted info:eu-repo/semantics/openAccess CC-BY Station Biologique de Roscoff BIOACID Biological Impacts of Ocean Acidification Class EPOCA European Project on Ocean Acidification Experimental treatment Experiment day Family Fraction Fraction of sample Kingdom Number of sequences Order Phylum Sample ID Sequence abundance Dataset 2010 ftpangaea https://doi.org/10.1594/PANGAEA.777733 https://doi.org/10.1594/PANGAEA.769833 2023-01-20T09:43:08Z 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 PANGAEA - Data Publisher for Earth & Environmental Science Svalbard |
institution |
Open Polar |
collection |
PANGAEA - Data Publisher for Earth & Environmental Science |
op_collection_id |
ftpangaea |
language |
English |
topic |
BIOACID Biological Impacts of Ocean Acidification Class EPOCA European Project on Ocean Acidification Experimental treatment Experiment day Family Fraction Fraction of sample Kingdom Number of sequences Order Phylum Sample ID Sequence abundance |
spellingShingle |
BIOACID Biological Impacts of Ocean Acidification Class EPOCA European Project on Ocean Acidification Experimental treatment Experiment day Family Fraction Fraction of sample Kingdom Number of sequences Order Phylum Sample ID Sequence abundance De Vargas, Colomban Bittner, Lucie Svalbard 2010 mesocosm experiment: Protistan diversity |
topic_facet |
BIOACID Biological Impacts of Ocean Acidification Class EPOCA European Project on Ocean Acidification Experimental treatment Experiment day Family Fraction Fraction of sample Kingdom Number of sequences Order Phylum Sample ID Sequence abundance |
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 |
publishDate |
2010 |
url |
https://doi.pangaea.de/10.1594/PANGAEA.777733 https://doi.org/10.1594/PANGAEA.777733 |
geographic |
Svalbard |
geographic_facet |
Svalbard |
genre |
Ocean acidification Svalbard |
genre_facet |
Ocean acidification Svalbard |
op_source |
Station Biologique de Roscoff |
op_relation |
https://doi.org/10.1594/PANGAEA.769833 https://doi.pangaea.de/10.1594/PANGAEA.777733 https://doi.org/10.1594/PANGAEA.777733 |
op_rights |
CC-BY-3.0: Creative Commons Attribution 3.0 Unported Access constraints: unrestricted info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1594/PANGAEA.777733 https://doi.org/10.1594/PANGAEA.769833 |
_version_ |
1766157569718484992 |