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133 results for “Amplicon sequencing”
Supplementary material 1 from: Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G (2019) PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 53: 73-91. https://doi.org/10.3897/mycokeys.53.34761
: Data type: measurement
Data from: Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus
The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that: i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod endosymbiont studies.
Supplementary material 1 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691
Scripts used for metabarcoding analysis
Supplementary material 2 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691
Figure S1, Tables S1, S2
Data from: From benchtop to desktop: important considerations when designing amplicon sequencing workflows
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Data from: A sequel to Sanger: amplicon sequencing that scales
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Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility
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Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing
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Data from: More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing
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Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?
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Data from: Genotyping SNPs and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms
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Data from: Genotyping-in-Thousands by sequencing (GT-seq): a cost effective SNP genotyping method based on custom amplicon sequencing
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Data from: Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus
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Data from: Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly
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Data from: Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)
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An amplicon sequencing protocol for attacker identification from DNA traces left on artificial prey
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Epigenetic age-predictions in mice using pyrosequencing, droplet digital PCR or barcoded bisulfite amplicon sequencing
GEO Series GSE156193. Mus musculus. 111 samples. Type: Methylation profiling by high throughput sequencing.
Targeted Amplicon Sequencing: The Interferon γ Pathway Enhances Pluripotency and X-Chromosome Reactivation in iPSC Reprogramming
GEO Series GSE255928. Mus musculus. 4 samples. Type: Other.
Highly sensitive amplicon-based transcript quantification by semi-conductor sequencing
GEO Series GSE58737. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Amplicon-based bisulfite sequencing of promoter regions for selected tumour supressor genes in DNA from white blood cells.
GEO Series GSE201688. Homo sapiens. 19 samples. Type: Methylation profiling by high throughput sequencing.
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