Illumina Miseq
Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity
... In the past, studies on the microbial composition of freshwater sponges were limited to the culture based iden- tification (Parfenova et al. 2008), 16S rRNA clone library (Kaluzhnaya et al. 2012), DGGE analysis (Costa et ...
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Cross clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq
... Antiretroviral therapy has been shown to be the most potent intervention for both treating and preventing HIV [1,2]. However, the effectiveness of antiretroviral drugs is threatened by the development and transmission of ...
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Research on the Microbial Community Structure of Wooden Relics and the Preservation of Water Environment: Illumina MiSeq Sequencing
... DNA was extracted from samples using the improved method for CTAB [10]. The extracted DNA was amplified using a set of bar-coded primers 515F and 806R. The PCR products from each sample were pooled together with equal ...
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An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
... The Illumina MiSeq platform (San Diego, CA, USA) provides researchers with a scalable, high-throughput and streamlined sequencing platform to survey com- munity composition from clinical and environmental ...
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Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform
... Methods and results: Six dogs fed a natural diet and five dogs fed a commercial feed were selected; dog fecal metagenomic DNA samples were analyzed using the Illumina MiSeq platform. Pronounced differences ...
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Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique
... The aim of the present study was to evaluate the plaque microbiota in children with high prevalence of EBS and who had no EBS by using the Illumina MiSeq, thereby identifying a potential role for the ...
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A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non model species
... The same 21 MHC-I alleles were found in both the 454 and MiSeq datasets (Additional file 1: Figure S2). 19 of these alleles have been previously found in other house sparrow individuals, supporting the validity of ...
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Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data
... command. MiSeq sequencing generates paired-end reads with the potential for errors in the paired region of the sequences as previ- ously described ...large Illumina data sets, the ...
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BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome
... A recommended sequencing strategy for BAC pools. Using MTP as a guide, BAC clones were selected, pooled without the necessity of barcoding and used to prepare a sequencing library. NGS of BACs has been a viable option ...
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Different types of dates in saudi arabia and its most fungal spoilage and its most preservation methods
... Postharvest fruit spoilage bacteria and fungi associated with date palm (Phoenix dactylifera L) from Saudi Arabia.. Illumina MiSeq sequencing analysis of fungal diversity in st[r] ...
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Modulation of the human gut microbiota by dietary fibres occurs at the species level
... The data obtained from Illumina MiSeq sequencing was analyzed using the mothur software package [44] and their MiSeq SOP [45]. Forward and reverse reads generated by sequencing were assembled into ...
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Neonatal Sulfhemoglobinemia and Hemolytic Anemia Associated With Intestinal Morganella morganii
... microbiota compositional analysis via Illumina MiSeq sequencing where we noted the presence of M morganii. This species represented 38% of the relative abundance in the fecal microbiota of our subject, ...
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PubMedCentral-PMC5069770.pdf
... of Illumina reads (33), we modified the SISPA protocol by adding either 3 N’s or 4 N’s to the 5= ends of the SISPA PCR primers for each barcode, and using an equimolar combination of these modified primers during ...
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Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform
... the Illumina MiSeq platform and the 2-step PCR procedure sequenced on both the Illumina MiSeq and HiSeq ...the Illumina HiSeq and MiSeq platforms, we also sought to measure (i) ...
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<p>Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype</p>
... the Illumina MiSeq sequencing platform, to identify resistances to various DAAs between our iso- late and the wild-type replicons 1a and 1b, used as references (Table ...
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The complete genome sequence and analysis of vB_VorS-PVo5, a Vibrio phage infectious to the pathogenic bacterium Vibrio ordalii ATCC-33509
... The genome was sequenced on an Illumina MiSeq plat- form at the MR-DNA Laboratory (Shallowater, TX). The library for each sample was prepared using a Nextera DNA Sample Preparation Kit (Illumina), ...
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Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China
... Each of the 78 DNA samples was amplified separately using the fungal PCR primers ITS1F (5=-CTTG GTCATTTAGAGGAAGTAA-3=) and ITS2 (5=-GCTGCGTTCTTCATCGATGC-3=) (55) that target the internal transcribed spacer 1 (ITS1) ...
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Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium
... with Illumina MiSeq generating average read lengths of 250 base pairs in this ...to Illumina sequencing data [46, 47], especially concern- ing homopolymer regions between two and fourteen base pairs ...
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Endophytes of Pseudowintera colorata (horopito)
... 119 groups. For future studies, additional sites with adjacent immature and mature plants need to be sampled to get a conclusive understanding of the effect of plant maturity and location on endophyte communities. In ...
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DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs
... add Illumina sequencing adaptors to the amplified ITS2 sequences, the second PCR reaction was performed with fusion primers containing P5/P7 Illumina adaptors, 8-mer index sequences for sample ...
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