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133
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ShareScore release 0.9.0
Dataset results
133 results for “Amplicon sequencing”
Bisulfite amplicon sequencing can detect Glia and Neuron cell-free DNA in blood plasma.
GEO Series GSE126663. Homo sapiens. 81 samples. Type: Methylation profiling by high throughput sequencing.
Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
GEO Series GSE113675. Mus musculus; Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
amplicon sequence analysis of iPSC-derived iNKT cells and primary iNKT cells
GEO Series GSE311015. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
SNP confirmation: Sequencing of PCR amplicons that contained potential biallelic SNPs in HD-B and DM1-A patient cells.
GEO Series GSE148181. Homo sapiens. 126 samples. Type: Other.
High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells
GEO Series GSE143466. Homo sapiens. 125 samples. Type: Other.
Targeted amplicon sequencing data from specified genomic amplicons
GEO Series GSE171470. Homo sapiens. 999 samples. Type: Other.
Specific silencing of pathogenic mRNA by a novel compact RNA-targeting tool TaqTth-hpRNA [Amplicon sequencing]
GEO Series GSE269593. Escherichia coli BL21. 2 samples. Type: Other.
Data from: Modular tagging of amplicons using a single PCR for high-throughput sequencing
High-throughput sequencing (HTS) of PCR amplicons is becoming the method of choice to sequence one or several targeted loci for phylogenetic and DNA barcoding studies. Although the development of HTS has allowed rapid generation of massive amounts of DNA sequence data, preparing amplicons for HTS remains a rate-limiting step. For example, HTS platforms require platform-specific adapter sequences to be present at the 5′ and 3′ end of the DNA fragment to be sequenced. In addition, short multiplex identifier (MID) tags are typically added to allow multiple samples to be pooled in a single HTS run. Existing methods to incorporate HTS adapters and MID tags into PCR amplicons are either inefficient, requiring multiple enzymatic reactions and clean-up steps, or costly when applied to multiple samples or loci (fusion primers). We describe a method to amplify a target locus and add HTS adapters and MID tags via a linker sequence using a single PCR. We demonstrate our approach by generating reference sequence data for two mitochondrial loci (COI and 16S) for a diverse suite of insect taxa. Our approach provides a flexible, cost-effective and efficient method to prepare amplicons for HTS.
Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing
1. The simplicity and cost efficiency of Illumina amplicon sequencing has greatly contributed to the advancement of DNA barcoding and metabarcoding applications. However, current amplicon sequencing based barcoding approaches are usually restricted to short, single-locus fragments, limiting their taxonomic and phylogenetic resolution. 2. Here, we establish a cost efficient and simple multiplex PCR protocol for arthropod systematics by Illumina amplicon sequencing. We introduce primer sets, including several new, generic primers, to reliably amplify nine loci across a wide range of arthropods. Using a diverse collection of arthropod species from 19 orders, we test loci for amplification efficiency and estimate the effect of cross-species amplification bias on taxon recovery from bulk community samples. We then explore the taxonomic and phylogenetic utility of the primer sets, focusing on a dataset of spiders that includes both deep and recent divergences. 3. The set of loci provides good phylogenetic support across a wide taxonomic spectrum, making it a useful addition to COI for resolving lineages within a comparative context. All loci recover sequences for the majority of arthropod taxa in separate PCRs. However, cross-species amplification bias in some primers prevents an exhaustive taxon recovery from bulk community samples. 4. Our protocol makes it possible to generate multilocus datasets for large numbers of arthropod taxa for a fraction of the price and workload of Sanger sequencing. This opens up the possibility for parallel phylogenetic and taxonomic analysis of large collections of arthropods, but also enables rapid exploratory analyses of target lineages. Primers for metabarcoding applications should be carefully evaluated for their performance in bulk community samples and chosen to minimize cross-species amplification bias.
16S rRNA gene and ITS2 region amplicon sequencing of GBP5 KO mice and WT littermates
<p>16S rRNA gene (v4) and ITS2 region amplicon sequencing of fecal microbiota of GBP5 KO mice and their littermate WT mice.</p>
LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis
<p>Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (Less OTU Scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences.</p>
18S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p>Illumina paired-end V9-18S raw reads (FASTQ format, 2 X 150 PE) were pre-processed with cutadapt and vsearch to remove primer sequences, trim low quality bases and unify mixed orientation reads produced in the ligation-based library preparation; the procedure was implemented in a custom bash script. Processed reads were then used to generate amplicon sequence variants (ASVs) using the DADA2 R library; the pipeline was adapted from the one described on the program website (<span><span><a href="https://benjjneb.github.io/dada2/tutorial.html" target="_blank" rel="noopener">https://benjjneb.github.io/dada2/tutorial.html</a></span></span>); no further quality filtering was implemented at this stage, except for discarding all reads with ambiguities (parameter maxN = 0 of function filterAndTrim). Filtered forward (F) and reverse (R) reads were used to train the error model and then denoised by applying the trained error model to generate ASVs. Finally, F and R reads were merged and checked for chimeras; allowing no mismatches in read merging (default parameter maxMismatch = 0 of function mergePairs). ASVs were then classified with BLAST against the PR2 v5.01 reference database, integrated with 1,293 sequences from GoN protist strains and fungi environmental sequences. Highest bit score matching with the best taxonomic resolution were then selected among the returned results.</p>
Association of Intestinal Microbiota and the Onset of Perianal Abscess Based on 16S RDNA Amplicon Sequencing
ClinicalTrials.gov study NCT05862129. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Modular tagging of amplicons using a single PCR for high-throughput sequencing
Open the record for dataset details and reuse information.
Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing
Open the record for dataset details and reuse information.
Data from: Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon-sequencing
Open the record for dataset details and reuse information.
Amplicon sequence variant tables of Donax gouldii microbiomes from Scripps Pier, La Jolla, CA, USA
Open the record for dataset details and reuse information.
Cytosine base editors induce prevalent unwanted out-of-protospacer editing and target-strand editing [Targeted amplicon sequencing]
GEO Series GSE152907. Homo sapiens. 176 samples. Type: Other.
16S rDNA Amplicon Sequencing Analysis of Polystyrene Microplastic Exposed Zebrafish Intestine
GEO Series GSE136108. Danio rerio. 12 samples. Type: Other.
Tailoring a CRISPR/Cas-based Epigenome Editor for Programmable Chromatin Acylation and Decreased Cytotoxicity [Targeting Amplicon Sequencing II]
GEO Series GSE289920. Homo sapiens. 8 samples. Type: Other.
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