illumina compatible adapters  (Integrated DNA Technologies)


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    Structured Review

    Integrated DNA Technologies illumina compatible adapters
    Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the <t>Illumina</t> HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007
    Illumina Compatible Adapters, supplied by Integrated DNA Technologies, used in various techniques. Bioz Stars score: 94/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    illumina compatible adapters - by Bioz Stars, 2020-02
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    Images

    1) Product Images from "Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms"

    Article Title: Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

    Journal: eLife

    doi: 10.7554/eLife.11888

    Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007
    Figure Legend Snippet: Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007

    Techniques Used: Sampling, Filtration, Sequencing

    Bacterioplankton diversity as assessed by 16S rRNA gene tag sequencing. Sampling : Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11'03''N, 7°54'00''E) using small research vessels ( http://www.awi.de/en/expedition/ships/more-ships.html ) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria for DNA extraction was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Biomass of the 0.2–3 µm bacterioplankton fraction was used for DNA extraction and subsequent 16S rRNA gene tag sequencing. 16S rRNA gene tag sequencing: A total of 142 samples were collected for the years 2010 to 2012. After DNA extraction, the V4 region of the 16S rRNA gene was amplified using the primers 515F (5' GTGCCAGCMGCCGCGGTAA 3') and 806R (5' GGACTACHVGGGTWTCTAAT 3') ( Caporaso et al., 2011 ). Sequencing was carried out on an Illumina (San Diego, CA, USA) MiSeq sequencer with and 2x250 bp chemistry. This dataset was complemented by 16S rRNA gene tags from 7 samples from our initial study on the 2009 spring bloom ( Teeling et al., 2012 ). DNA of these samples was amplified using the primers 314F (5’ CCTACGGGNGGCWGCAG 3') and 805R (5’ GACTACHVGGGTATCTAATCC 3') ( Herlemann et al., 2011 ) and sequenced on the 454 FLX Ti platform. Data analysis: All tag data were analyzed using the SILVAngs pipeline with the SILVA ( Quast et al., 2013 ) v119 database. The SAR92 clade was subsequently reclassified to comply with the recently released SILVA v123, where the SAR92 no longer belong to the order Alteromonadales . The corresponding abundance data is summarized in Supplementary file 5 . Time points from days 50 to 160 were plotted for all years. Panel A-P depict data that are analogous to the CARD-FISH data presented in Figure 3 , with addition of the Flavobacteriia genus Tenacibaculum (E-H). Panels Q-X show minor Gammaproteobacteria clades (Q-T) and Roseobacter clades together with miscellaneous other minor clades (U-X) that were not tested by CARD-FISH probes. DOI: http://dx.doi.org/10.7554/eLife.11888.006
    Figure Legend Snippet: Bacterioplankton diversity as assessed by 16S rRNA gene tag sequencing. Sampling : Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11'03''N, 7°54'00''E) using small research vessels ( http://www.awi.de/en/expedition/ships/more-ships.html ) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria for DNA extraction was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Biomass of the 0.2–3 µm bacterioplankton fraction was used for DNA extraction and subsequent 16S rRNA gene tag sequencing. 16S rRNA gene tag sequencing: A total of 142 samples were collected for the years 2010 to 2012. After DNA extraction, the V4 region of the 16S rRNA gene was amplified using the primers 515F (5' GTGCCAGCMGCCGCGGTAA 3') and 806R (5' GGACTACHVGGGTWTCTAAT 3') ( Caporaso et al., 2011 ). Sequencing was carried out on an Illumina (San Diego, CA, USA) MiSeq sequencer with and 2x250 bp chemistry. This dataset was complemented by 16S rRNA gene tags from 7 samples from our initial study on the 2009 spring bloom ( Teeling et al., 2012 ). DNA of these samples was amplified using the primers 314F (5’ CCTACGGGNGGCWGCAG 3') and 805R (5’ GACTACHVGGGTATCTAATCC 3') ( Herlemann et al., 2011 ) and sequenced on the 454 FLX Ti platform. Data analysis: All tag data were analyzed using the SILVAngs pipeline with the SILVA ( Quast et al., 2013 ) v119 database. The SAR92 clade was subsequently reclassified to comply with the recently released SILVA v123, where the SAR92 no longer belong to the order Alteromonadales . The corresponding abundance data is summarized in Supplementary file 5 . Time points from days 50 to 160 were plotted for all years. Panel A-P depict data that are analogous to the CARD-FISH data presented in Figure 3 , with addition of the Flavobacteriia genus Tenacibaculum (E-H). Panels Q-X show minor Gammaproteobacteria clades (Q-T) and Roseobacter clades together with miscellaneous other minor clades (U-X) that were not tested by CARD-FISH probes. DOI: http://dx.doi.org/10.7554/eLife.11888.006

    Techniques Used: Sequencing, Sampling, DNA Extraction, Filtration, Amplification, Fluorescence In Situ Hybridization

    Related Articles

    DNA Extraction:

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    Real-time Polymerase Chain Reaction:

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    RNA Extraction:

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    Sequencing:

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    Article Title: Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
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    Agarose Gel Electrophoresis:

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    Ligation:

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    Article Snippet: .. The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA Biosystems). .. The prepared libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

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    Article Snippet: .. The fragments were treated with end repair, A-tailing, and ligation of Illumina-compatible adapters (IDT, Inc.) using the Illumina library creation kit (Kapa Biosystems). .. For LMP, 5 µg of DNA was sheared using the g-TUBE (Covaris), and the gel size was selected for 4 kb.

    Article Title: Microbial Ecology on Solar Panels in Berkeley, CA, United States
    Article Snippet: .. The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc), and 5 cycles of PCR was used to enrich for the final library. .. The libraries were quantified and run on a Roche LightCycler 480 real-time PCR instrument, followed by preparation for sequencing on the Illumina HiSeq2500 sequencing platform using a TruSeq Rapid paired-end cluster kit, v.4.

    Article Title: Unexpected host dependency of Antarctic Nanohaloarchaeota
    Article Snippet: .. The fragments were treated with end repair, A tailing, and ligation of Illumina compatible adapters (IDT, Inc.) using the KAPA-Illumina library creation kit (KAPA Biosystems). qPCR was used to determine the concentration of the libraries before sequencing on the Illumina HiSeq-2500 to yield 150-bp paired end reads at the Department of Energy (DOE) Joint Genome Institute. ..

    Article Title: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors
    Article Snippet: .. The fragments were treated with end repair, A-tailing, and ligation of Illumina-compatible adapters (IDT, Inc.,) using the KAPA-Illumina library creation kit (KAPA biosystems). .. LMP was produced from 6 μg of DNA sheared using the Covaris g-TUBE™ (Covaris) and gel size selected for 4 kb.

    Article Title: Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California
    Article Snippet: .. The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA Biosystems). .. The prepared sample libraries were quantified by qPCR using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Article Title: Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass
    Article Snippet: .. Sheared DNA fragments were processed for ligation to Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA biosystems). .. For transcriptome, stranded cDNA libraries were generated using the Illumina Truseq Stranded RNA LT kit.

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    Article Snippet: .. The fragments were treated by end repair, A tailing, and ligation of Illumina compatible adapters (IDT, Inc.) with the KAPA-Illumina library creation kit (KAPA Biosystems). .. Paired-end reads of 250 bp were generated on an Illumina Hiseq2500 with sequencing depth enumerated in .

    Isolation:

    Article Title: Microbial Ecology on Solar Panels in Berkeley, CA, United States
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    Article Title: Unexpected host dependency of Antarctic Nanohaloarchaeota
    Article Snippet: Enrichment culture biomass was harvested by centrifugation at 5,000 × g , and DNA was isolated using a QIAGEN DNeasy Blood and Tissue Kit following the manufacturer’s instructions. .. The fragments were treated with end repair, A tailing, and ligation of Illumina compatible adapters (IDT, Inc.) using the KAPA-Illumina library creation kit (KAPA Biosystems). qPCR was used to determine the concentration of the libraries before sequencing on the Illumina HiSeq-2500 to yield 150-bp paired end reads at the Department of Energy (DOE) Joint Genome Institute.

    Next-Generation Sequencing:

    Article Title: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
    Article Snippet: The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA Biosystems). .. The prepared libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Article Title: Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
    Article Snippet: Subsequently, T-tailed adapters, containing sequences used during cluster formation and Illumina compatible adapters (IDT, San Jose, CA, USA), were ligated to the purified DNA fragments applying the KAPA-Illumina library creation kit (KAPA Biosystems, Wilmington, MA, USA). .. The prepared sample libraries were quantified applying the KAPA Biosystem’s next-generation sequencing library qPCR kit (KAPA Biosystems, Wilmington, MA, USA) and run on the Roche LightCycler 480 real-time PCR instrument (Roche Basel, Switzerland).

    Article Title: Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum
    Article Snippet: The selected fragments were then end repaired, A tailed, and ligated to Illumina compatible adapters (IDT, Inc) using KAPA-Illumina library creation kit (KAPA Biosystems). .. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Article Title: Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose
    Article Snippet: The selected fragments were then end repaired, A tailed, and ligated to Illumina compatible adapters (IDT, Inc) using KAPA’s Illumina library creation kit (KAPA Biosystems). .. Libraries were quantified using KAPA Biosystems next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Article Title: Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts
    Article Snippet: Illumina compatible adapters (IDT, Inc) were ligated to the mate paired fragments and 12 cycles of PCR was used to enrich for the final library (KAPA Biosystems). .. All prepared libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Article Title: Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California
    Article Snippet: The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA Biosystems). .. The prepared sample libraries were quantified by qPCR using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Article Title: Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485
    Article Snippet: The selected fragments were then end repaired, A tailed and ligated to Illumina compatible adapters (IDT, Inc) using KAPA-Illumina library creation kit (KAPA biosystems). .. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Generated:

    Article Title: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
    Article Snippet: The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA Biosystems). .. For metatranscriptomes, stranded cDNA libraries were generated using the Illumina Truseq Stranded RNA LT kit.

    Article Title: Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum
    Article Snippet: Unamplified libraries were generated using a modified version of Illumina’s standard protocol. .. The selected fragments were then end repaired, A tailed, and ligated to Illumina compatible adapters (IDT, Inc) using KAPA-Illumina library creation kit (KAPA Biosystems).

    Article Title: Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California
    Article Snippet: Metagenome sequencing and assembly A total of 51.7 Gbp were generated from the oil-associated microbiome. .. The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA Biosystems).

    Article Title: Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass
    Article Snippet: Sheared DNA fragments were processed for ligation to Illumina compatible adapters (IDT, Inc) using the KAPA-Illumina library creation kit (KAPA biosystems). .. For transcriptome, stranded cDNA libraries were generated using the Illumina Truseq Stranded RNA LT kit.

    Article Title: The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
    Article Snippet: The fragments were treated by end repair, A tailing, and ligation of Illumina compatible adapters (IDT, Inc.) with the KAPA-Illumina library creation kit (KAPA Biosystems). .. Paired-end reads of 250 bp were generated on an Illumina Hiseq2500 with sequencing depth enumerated in .

    Article Title: Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485
    Article Snippet: Unamplified libraries were generated using a modified version of Illumina’s standard protocol. .. The selected fragments were then end repaired, A tailed and ligated to Illumina compatible adapters (IDT, Inc) using KAPA-Illumina library creation kit (KAPA biosystems).

    Spectrophotometry:

    Article Title: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors
    Article Snippet: Quality control was ensured by agarose gel migration and by NanoDrop1000 spectrophotometer quality assay (Thermo Fisher Scientific, Wilmington, U.S.A.). .. The fragments were treated with end repair, A-tailing, and ligation of Illumina-compatible adapters (IDT, Inc.,) using the KAPA-Illumina library creation kit (KAPA biosystems).

    Purification:

    Article Title: Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
    Article Snippet: .. Subsequently, T-tailed adapters, containing sequences used during cluster formation and Illumina compatible adapters (IDT, San Jose, CA, USA), were ligated to the purified DNA fragments applying the KAPA-Illumina library creation kit (KAPA Biosystems, Wilmington, MA, USA). .. The prepared sample libraries were quantified applying the KAPA Biosystem’s next-generation sequencing library qPCR kit (KAPA Biosystems, Wilmington, MA, USA) and run on the Roche LightCycler 480 real-time PCR instrument (Roche Basel, Switzerland).

    Article Title: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors
    Article Snippet: In brief, the protocol consisted in a crude extraction using CTAB buffer followed by a purification step using Qiagen 5,000/G Genomic Tips (Qiagen, Courtaboeuf, France). .. The fragments were treated with end repair, A-tailing, and ligation of Illumina-compatible adapters (IDT, Inc.,) using the KAPA-Illumina library creation kit (KAPA biosystems).

    Produced:

    Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
    Article Snippet: Fragment libraries were produced from 100 ng genomic DNA (gDNA) sheared to 300 bp using the Covaris LE220 instrument and size selected using solid-phase reversible immobilization (SPRI) beads (Beckman Coulter). .. The fragments were treated with end repair, A-tailing, and ligation of Illumina-compatible adapters (IDT, Inc.) using the Illumina library creation kit (Kapa Biosystems).

    Article Title: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors
    Article Snippet: The fragments were treated with end repair, A-tailing, and ligation of Illumina-compatible adapters (IDT, Inc.,) using the KAPA-Illumina library creation kit (KAPA biosystems). .. LMP was produced from 6 μg of DNA sheared using the Covaris g-TUBE™ (Covaris) and gel size selected for 4 kb.

    Polymerase Chain Reaction:

    Article Title: Microbial Ecology on Solar Panels in Berkeley, CA, United States
    Article Snippet: .. The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc), and 5 cycles of PCR was used to enrich for the final library. .. The libraries were quantified and run on a Roche LightCycler 480 real-time PCR instrument, followed by preparation for sequencing on the Illumina HiSeq2500 sequencing platform using a TruSeq Rapid paired-end cluster kit, v.4.

    Article Title: Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts
    Article Snippet: .. Illumina compatible adapters (IDT, Inc) were ligated to the mate paired fragments and 12 cycles of PCR was used to enrich for the final library (KAPA Biosystems). .. All prepared libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

    Incubation:

    Article Title: Microbial Ecology on Solar Panels in Berkeley, CA, United States
    Article Snippet: Briefly, pellets were thawed on ice, incubated with lysozyme in the PowerBead tubes solution without the beads (PowerSoil, MoBio) at 37°C for 10 min, and then transferred back to the PowerBead tubes containing the beads. .. The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc), and 5 cycles of PCR was used to enrich for the final library.

    Migration:

    Article Title: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors
    Article Snippet: Quality control was ensured by agarose gel migration and by NanoDrop1000 spectrophotometer quality assay (Thermo Fisher Scientific, Wilmington, U.S.A.). .. The fragments were treated with end repair, A-tailing, and ligation of Illumina-compatible adapters (IDT, Inc.,) using the KAPA-Illumina library creation kit (KAPA biosystems).

    Concentration Assay:

    Article Title: Unexpected host dependency of Antarctic Nanohaloarchaeota
    Article Snippet: .. The fragments were treated with end repair, A tailing, and ligation of Illumina compatible adapters (IDT, Inc.) using the KAPA-Illumina library creation kit (KAPA Biosystems). qPCR was used to determine the concentration of the libraries before sequencing on the Illumina HiSeq-2500 to yield 150-bp paired end reads at the Department of Energy (DOE) Joint Genome Institute. ..

    Modification:

    Article Title: Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum
    Article Snippet: Unamplified libraries were generated using a modified version of Illumina’s standard protocol. .. The selected fragments were then end repaired, A tailed, and ligated to Illumina compatible adapters (IDT, Inc) using KAPA-Illumina library creation kit (KAPA Biosystems).

    Article Title: Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485
    Article Snippet: Unamplified libraries were generated using a modified version of Illumina’s standard protocol. .. The selected fragments were then end repaired, A tailed and ligated to Illumina compatible adapters (IDT, Inc) using KAPA-Illumina library creation kit (KAPA biosystems).

    Centrifugation:

    Article Title: Unexpected host dependency of Antarctic Nanohaloarchaeota
    Article Snippet: Enrichment culture biomass was harvested by centrifugation at 5,000 × g , and DNA was isolated using a QIAGEN DNeasy Blood and Tissue Kit following the manufacturer’s instructions. .. The fragments were treated with end repair, A tailing, and ligation of Illumina compatible adapters (IDT, Inc.) using the KAPA-Illumina library creation kit (KAPA Biosystems). qPCR was used to determine the concentration of the libraries before sequencing on the Illumina HiSeq-2500 to yield 150-bp paired end reads at the Department of Energy (DOE) Joint Genome Institute.

    Genomic Sequencing:

    Article Title: Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485
    Article Snippet: Paragraph title: Genomic sequencing ... The selected fragments were then end repaired, A tailed and ligated to Illumina compatible adapters (IDT, Inc) using KAPA-Illumina library creation kit (KAPA biosystems).

    Derivative Assay:

    Article Title: Unexpected host dependency of Antarctic Nanohaloarchaeota
    Article Snippet: The fragments were treated with end repair, A tailing, and ligation of Illumina compatible adapters (IDT, Inc.) using the KAPA-Illumina library creation kit (KAPA Biosystems). qPCR was used to determine the concentration of the libraries before sequencing on the Illumina HiSeq-2500 to yield 150-bp paired end reads at the Department of Energy (DOE) Joint Genome Institute. .. Assembly of the enrichment culture metagenome yielded 28,529 scaffolds (maximum length = 136,362 bp, scaffold N50 = 53,057 bp), which derived from 2 main taxa: Hrr. lacusprofundi 670-fold average read depth (28% relative abundance) and Nanohaloarchaeota 983-fold average read depth (41% relative abundance).

    Hybridization:

    Article Title: Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts
    Article Snippet: The adapter ligated DNA fragments were circularized by intra-molecular hybridization. .. Illumina compatible adapters (IDT, Inc) were ligated to the mate paired fragments and 12 cycles of PCR was used to enrich for the final library (KAPA Biosystems).

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    Integrated DNA Technologies illumina compatible adapters
    Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the <t>Illumina</t> HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007
    Illumina Compatible Adapters, supplied by Integrated DNA Technologies, used in various techniques. Bioz Stars score: 94/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007

    Journal: eLife

    Article Title: Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

    doi: 10.7554/eLife.11888

    Figure Lengend Snippet: Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007

    Article Snippet: The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Coralville, IA, USA) using the KAPA-Illumina library creation kit.

    Techniques: Sampling, Filtration, Sequencing

    Bacterioplankton diversity as assessed by 16S rRNA gene tag sequencing. Sampling : Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11'03''N, 7°54'00''E) using small research vessels ( http://www.awi.de/en/expedition/ships/more-ships.html ) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria for DNA extraction was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Biomass of the 0.2–3 µm bacterioplankton fraction was used for DNA extraction and subsequent 16S rRNA gene tag sequencing. 16S rRNA gene tag sequencing: A total of 142 samples were collected for the years 2010 to 2012. After DNA extraction, the V4 region of the 16S rRNA gene was amplified using the primers 515F (5' GTGCCAGCMGCCGCGGTAA 3') and 806R (5' GGACTACHVGGGTWTCTAAT 3') ( Caporaso et al., 2011 ). Sequencing was carried out on an Illumina (San Diego, CA, USA) MiSeq sequencer with and 2x250 bp chemistry. This dataset was complemented by 16S rRNA gene tags from 7 samples from our initial study on the 2009 spring bloom ( Teeling et al., 2012 ). DNA of these samples was amplified using the primers 314F (5’ CCTACGGGNGGCWGCAG 3') and 805R (5’ GACTACHVGGGTATCTAATCC 3') ( Herlemann et al., 2011 ) and sequenced on the 454 FLX Ti platform. Data analysis: All tag data were analyzed using the SILVAngs pipeline with the SILVA ( Quast et al., 2013 ) v119 database. The SAR92 clade was subsequently reclassified to comply with the recently released SILVA v123, where the SAR92 no longer belong to the order Alteromonadales . The corresponding abundance data is summarized in Supplementary file 5 . Time points from days 50 to 160 were plotted for all years. Panel A-P depict data that are analogous to the CARD-FISH data presented in Figure 3 , with addition of the Flavobacteriia genus Tenacibaculum (E-H). Panels Q-X show minor Gammaproteobacteria clades (Q-T) and Roseobacter clades together with miscellaneous other minor clades (U-X) that were not tested by CARD-FISH probes. DOI: http://dx.doi.org/10.7554/eLife.11888.006

    Journal: eLife

    Article Title: Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

    doi: 10.7554/eLife.11888

    Figure Lengend Snippet: Bacterioplankton diversity as assessed by 16S rRNA gene tag sequencing. Sampling : Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11'03''N, 7°54'00''E) using small research vessels ( http://www.awi.de/en/expedition/ships/more-ships.html ) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria for DNA extraction was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Biomass of the 0.2–3 µm bacterioplankton fraction was used for DNA extraction and subsequent 16S rRNA gene tag sequencing. 16S rRNA gene tag sequencing: A total of 142 samples were collected for the years 2010 to 2012. After DNA extraction, the V4 region of the 16S rRNA gene was amplified using the primers 515F (5' GTGCCAGCMGCCGCGGTAA 3') and 806R (5' GGACTACHVGGGTWTCTAAT 3') ( Caporaso et al., 2011 ). Sequencing was carried out on an Illumina (San Diego, CA, USA) MiSeq sequencer with and 2x250 bp chemistry. This dataset was complemented by 16S rRNA gene tags from 7 samples from our initial study on the 2009 spring bloom ( Teeling et al., 2012 ). DNA of these samples was amplified using the primers 314F (5’ CCTACGGGNGGCWGCAG 3') and 805R (5’ GACTACHVGGGTATCTAATCC 3') ( Herlemann et al., 2011 ) and sequenced on the 454 FLX Ti platform. Data analysis: All tag data were analyzed using the SILVAngs pipeline with the SILVA ( Quast et al., 2013 ) v119 database. The SAR92 clade was subsequently reclassified to comply with the recently released SILVA v123, where the SAR92 no longer belong to the order Alteromonadales . The corresponding abundance data is summarized in Supplementary file 5 . Time points from days 50 to 160 were plotted for all years. Panel A-P depict data that are analogous to the CARD-FISH data presented in Figure 3 , with addition of the Flavobacteriia genus Tenacibaculum (E-H). Panels Q-X show minor Gammaproteobacteria clades (Q-T) and Roseobacter clades together with miscellaneous other minor clades (U-X) that were not tested by CARD-FISH probes. DOI: http://dx.doi.org/10.7554/eLife.11888.006

    Article Snippet: The fragments were treated with end-repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Coralville, IA, USA) using the KAPA-Illumina library creation kit.

    Techniques: Sequencing, Sampling, DNA Extraction, Filtration, Amplification, Fluorescence In Situ Hybridization