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120
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Dataset results
120 results for “barcode sequence”
CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [mixed Sample of cell lines and organisms]
GEO Series GSE153113. Homo sapiens; Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
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.
Figure 5 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 5 - Intraspecific COI variability (K2P): maximum pairwise distances; Chilopoda
Figure 3 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 3 - Interspecific COI variability (K2P): distance to nearest neighbour; Chilopoda
Figure 6 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 6 - Intraspecific COI variability (K2P): maximum pairwise distances; Diplopoda
Figure 4 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 4 - Interspecific COI variability (K2P): distance to nearest neighbour; Diplopoda
CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [snATAC-seq]
GEO Series GSE165048. Homo sapiens. 192 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4 T cell clones from murine tissues
GEO Series GSE240041. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [PBMC_perf_10X]
GEO Series GSE218208. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing
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CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [scRNA-seq]
GEO Series GSE165047. Canis lupus familiaris; Drosophila melanogaster; Rattus norvegicus; Chlorocebus sabaeus; Homo sapiens; Cricetulus griseus; Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing
GEO Series GSE116453. Escherichia coli ATCC 8739. 1 samples. Type: Expression profiling by high throughput sequencing.
Microbial single-cell RNA sequencing by split-pool barcoding
GEO Series GSE151940. Bacillus subtilis; Escherichia coli. 3 samples. Type: Expression profiling by high throughput sequencing.
Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing [snRNA-seq, ssRNA-seq]
GEO Series GSE312903. Mus musculus. 47 samples. Type: Expression profiling by high throughput sequencing.
Single cell sequencing and retrograde barcode tracing reveal human DA neuron identities based on projection patterns in stem cell-derived grafts
GEO Series GSE233885. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing.
MinION-in-ARMS: Nanopore sequencing to expedite barcoding of specimen-rich macrofaunal samples from Autonomous Reef Monitoring Structures
<p>DNA basecalling, demultiplexing information and sequence barcodes</p>
RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [scRNA-seq_ScaleUp_Scipio]
GEO Series GSE218212. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Mapping diverse RNA modifications simulataneously by proximity barcode sequencing
GEO Series GSE278242. Homo sapiens. 54 samples. Type: Other.
Cross-amplified Barcodes on Slides for Spatial Transcriptomics Sequencing
GEO Series GSE211858. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing; Other.
Split-pool combinatorial barcoding sequencing of murine immune cells
GEO Series GSE253406. Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing.
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