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253
datasets available to search
ShareScore release 0.9.0
Dataset results
253 results for “amplicons”
An NPAS4:NuA4 complex couples synaptic activity to DNA repair [SiMSen-Seq (amplicon)]
GEO Series GSE175948. Mus musculus. 11 samples. Type: Other.
Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [Amplicon]
GEO Series GSE171678. Homo sapiens. 10 samples. Type: Other.
Amplicon-seq of SVA methylation in human sperm
GEO Series GSE174562. Homo sapiens. 5 samples. Type: Methylation profiling by high throughput sequencing.
Targeted amplicon sequencing data from specified genomic amplicons
GEO Series GSE171470. Homo sapiens. 999 samples. Type: Other.
The quantitative impact of 3′UTRs on gene expression [amplicon-seq]
GEO Series GSE270252. Homo sapiens. 99 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.
An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [Amplicon-seq]
GEO Series GSE141491. Homo sapiens. 33 samples. Type: Other.
Genome position and gene amplification - higher resolution mapping of amplicons
GEO Series GSE6360. Homo sapiens. 6 samples. Type: Genome variation profiling by genome tiling array.
Data from: A broadly applicable COI primer pair and an efficient single‐tube amplicon library preparation protocol for metabarcoding
The nucleotide variation in the cytochrome c oxidase subunit I (COI) gene makes it ideal for assigning sequences to species. However, this variability also makes it difficult to design truly universal primers. Here, we present the forward primer "Sauron-S878", specifically designed to facilitate library preparation for metabarcoding. This primer is modified to improve the coverage of terrestrial species compared to the primer mCOIintF, optimized for aquatic systems, which raised the in-silico coverage from 74.4% to 98.3% of available NCBI sequences (perfect match in 3'-region, up to 3 mismatches in remaining primer). When paired with the reverse primer "jgHCO2198" (fragment length ~313 bp) these primers amplified 98.4% of 255 tested DNA extracts from various taxa, which is better than many other common COI barcoding primers. Furthermore, a single tube protocol was developed, wherein these primers amplify the target gene, and attach MIDs and Illumina sequencing adapters in one reaction. This eliminates the need for re-amplification or enzymatic ligation during library preparation while keeping the flexibility to modularly combine primers and MIDs. Using the single tube approach, three replicates of three mock samples were sequenced on a MiSeq platform with no adverse effects compared to commercial Nextera indexing kits. From this run 75% of all included taxa could be recovered, with no considerable bias among taxonomic groups. Despite the fact that 98.4% of the extracts were confirmed to amplify in-vitro, this number was lower than expected. A reason for this discrepancy was a clear link between the relative concentration of a specific DNA type in the template and the number of returned reads for this DNA. We would argue that such a bias may be especially problematic in metabarcoding where samples usually contain trace DNA in unknown amounts. However, how this affects the completeness of metabarcoding results has yet been poorly investigated.
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>
Pilot Project: The Amplicon and Metatranscriptomic Study of Intra and Extra Intestinal Microbiome in Non-infectious Uveitis Disease
ClinicalTrials.gov study NCT04126850. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.
Characterization of maturational enhancer activity by massively parallel reporter assay [amplicon-Seq]
GEO Series GSE196346. Mus musculus; Adeno-associated virus 9. 88 samples. Type: Other.
Evaluation of Wpa-generated amplicons for SNP typing (allele bias), locus bias, and detection of known CNVs
GEO Series GSE12751. Homo sapiens. 19 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array; Genome variation profiling by genome tiling array.
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: A broadly applicable COI primer pair and an efficient single‐tube amplicon library preparation protocol for metabarcoding
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.