Data from: A next-generation sequencing approach to river biomonitoring using benthic diatoms

Kermarrec L, Franc A, Rimet F, Chaumeil P, Frigerio J, Humbert J, Bouchez A

Date Published: February 3, 2014

DOI: http://dx.doi.org/10.5061/dryad.3gm8c

 

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Title LACL1
Downloaded 10 times
Description Benthic sample from Lay river on Mainland France that usually displays high diversity of diatom taxa. Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs. After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions. Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
Download Pool1.RL3.clean.sff_extract.fasta (40.40 Mb)
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Title BDNA
Downloaded 6 times
Description Benthic sample from Saint-Denis river on French tropical islands in the Indian Ocean (la Réunion) that usually displays low diversity of diatom taxa. Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs. After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions. Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
Download Pool1.RL7.clean.sff_extract.fasta (55.07 Mb)
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Title LACL2
Downloaded 5 times
Description Benthic sample from Lay river on Mainland France that usually displays high diversity of diatom taxa. Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs. After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions. Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
Download Pool1.RL4.clean.sff_extract.fasta (73.85 Mb)
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Title CHLO
Downloaded 5 times
Description Benthic sample from Chiers river on Mainland France that usually displays low diversity of diatom taxa. Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs. After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions. Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
Download Pool1.RL5.clean.sff_extract.fasta (79.88 Mb)
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Title COIN
Downloaded 12 times
Description Benthic sample from Coconi river on French tropical islands in the Indian Ocean (Mayotte) that usually displays high diversity of diatom taxa. Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs. After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions. Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
Download Pool1.RL6.clean.sff_extract.fasta (92.45 Mb)
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When using this data, please cite the original publication:

Kermarrec L, Franc A, Rimet F, Chaumeil P, Frigerio J, Humbert J, Bouchez A (2014) A next-generation sequencing approach to river biomonitoring using benthic diatoms. Freshwater Science 33(1): 349-363. http://dx.doi.org/10.1086/675079

Additionally, please cite the Dryad data package:

Kermarrec L, Franc A, Rimet F, Chaumeil P, Frigerio J, Humbert J, Bouchez A (2014) Data from: A next-generation sequencing approach to river biomonitoring using benthic diatoms. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3gm8c
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