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17 results for “DNA target enrichment”
Data from: Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR ‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics
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Figure 10 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 10. Mantidactylus (Mantidactylus) radaka sp. nov. being prepared for human consumption. (a) Frogs and crabs are collected from broad streams. Then (b) the frogs are gutted and skinned, and the head, hands and feet removed. The frog is then rinsed in the stream, leaving (c) cleaned animals for cooking in a stew. Note the ovaries full with hundreds of eggs.
Figure 9 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 9. Preserved type specimens of the four nomina in the Mantidactylus subgenus Mantidactylus and one of the paralectotypes of Rana guttulata.
Figure 7 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 7. Photographs of living specimens of Mantidactylus (Mantidactylus) guttulatus, M. (M.) grandidieri, and of three candidate species. (a, b) M. (M.) guttulatus, female ZSM 1013/2003 (FGMV 2002.438) from Ranomafana. (c) Unidentified specimen from Ranomafana, assigned tentatively to M. (M.) guttulatus (no genetic evidence). (d, e) M. (M.) guttulatus, specimen KU 340853 (CRH729) from Ranomafana. (f) M. (M.) grandidieri, specimen ZSM 5077/2005 (ZCMV 2159) from Nosy Mangabe. (g) M. (M.) grandidieri, specimen ZSM 276/2005 (FGZC 2682) from Vohidrazana. (h) M. (M.) grandidieri, unidentified specimen (probably subadult) from Andranofotsy. (i, j) M. (M.) grandidieri, specimen KU
Figure 5. Per-base coverage plots for the 16S in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 5. Per-base coverage plots for the 16S fragment in four Mantidactylus type specimens from the MNHN and BMNH collections. (a) BMNH 1947.2.25.48 (paralectotype of Rana guttulata); (b) BMNH 1947.2.25.51 (paralectotype of Rana guttulata); (c) MNHN 1895.255 (syntype of M. grandidieri); (d) MNHN 1883.520 (syntype of M. grandidieri).
Figure 3 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 3. Haplotype network of the subgenus Mantidactylus based on 1227 bp of the nuclear RAG-1 gene from 39 samples. Small black dots represent additional mutational steps.
Figure 2 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 2. Diagonal matrix visualising the mean uncorrected genetic distances (p-distances) in the mitochondrial 16S rRNA gene between the different lineages in the subgenus Mantidactylus, calculated from 514 bp of the 16S mitochondrial gene.
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 bp of the mitochondrial 16S rRNA gene. The values at the nodes are the bootstrap supports (not given for intra-lineage nodes for improved clarity). The type specimens of M. guttulatus and M. grandidieri from the London and Paris museum collections are highlighted in red and brown, respectively.
Figure 4 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 4. Stacked barplots showing the number of reads uniquely matching different reference sequences for the three targeted mitochondrial genes with a similarity threshold of 98%. The Rana pigra type was not included because the number of reads was too low.
Figure 8 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 8. Lateral views of the heads of preserved adult males of Mantidactylus (Mantidactylus) radaka sp. nov. in comparison with M. (M.) guttulatus and M. (M.) grandidieri. Note the more distinct and larger tympanum (indicated by yellow arrows) in the latter two species. Not to scale.
Figure 6 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 6. Photographs of living specimens of Mantidactylus radaka sp. nov. (a, b) Male holotype ZSM 644/2001 (field number FGMV 2001.132) from Manarikoba forest, Tsaratanana Massif. (c–f) Female paratype ZSM 1800/2010 (ZCMV 12345) from Camp 1 (Antevialambazaha), Tsaratanana Massif. (g, h) Female paratype ZSM 97/2016 (MSZC 0080) from Ampotsidy. (i, j) Male paratype MSZC 0120 (uncatalogued in UADBA) from Ampotsidy. (k) Unidentified specimen from Camp 0 (Ankijagna Lagnana), Tsaratanana Massif. (l) Paratype ZSM 582/2014 (DRV 6073) from Camp 0 (Ankijagna Lagnana). (m, n) Unidentified female specimen from Manongarivo (Camp 0), probably preserved in UADBA collection.
Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
<p>The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family's major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we present a phylogeny inferred from nucleotide sequence data of 492 nuclear single-copy genes (230,915 aligned amino acid sites) from 94 species of Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae, Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target enrichment data. We find support for Amiseginae being more closely related to Cleptinae than to Chrysidinae. Furthermore, we find strong support for Allocoeliini being the sister lineage of all remaining Chrysidinae, while Elampini represent the sister lineage of Chrysidini and Parnopini. Our study corroborates results from a recent phylogenomic investigation which revealed Chrysidoidea as likely paraphyletic</p>
Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
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Targeting DNA Methylation Depletes Uterine Leiomyoma Stem Cell-enriched Population by Stimulating Their Differentiation
GEO Series GSE138051. Homo sapiens. 45 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Targeted DNA Sequencing of Circulating Tumor Cell-Enriched Samples from Stage II/III NSCLC Patients
<p>Targeted DNA sequencing of circulating tumor cell (CTC) enriched blood samples from stage II/III non-small cell lung cancer (NSCLC) patients prior to undergoing chemoradiation and immunotherapy treatment. The CTC samples were enriched using a label-free microfluidic platform, the Labyrinth. Following enrichment, the samples were fixed in 80% methanol or ethanol and stored at -80C or -20C, respectively. DNA was extracted from the samples using Qiagen's DNA/RNA AllPrep kit and submitted to the Univeristy of Michigan's Advanced Genomics Core (AGC) to perform targeted DNA sequencing using Illumina's TruSight Oncology (TSO) 500 assay. The TSO 500 assay consists of a 523 gene panel of specific oncogenes. Following sequecing, the pair-end fastq files were locally processed through the TSO 500 analysis pipeline (version: ruo-2.2.0.12) to produce the CombinedVariantOutput files per patient. Each file contains a list of all variants detected within the patient. For each variant, the following information is provided: gene name, chromosome, genomic position, reference call, alternative call, allele frequency, depth, p-dot notation, c-dot notation, consequence of variant, and the number of affected exons.</p>
Direct genetic transformation bypasses tumor-associated DNA methylation alterations (target enrichment)
GEO Series GSE276082. Mus musculus. 7 samples. Type: Methylation profiling by high throughput sequencing.
Reduced Retinal Microvascular Density, Improvement in Forepaw Reach, Comparative Microarray and Gene Set Enrichment Analysis using DNA Enzyme Targeting c-jun mRNA
GEO Series GSE37898. Mus musculus. 4 samples. Type: Expression profiling by array.
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Allen Brain Atlas
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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
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