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15 results for “DNA fingerprinting”
Supplementary Datasets for "Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints"
<p>Supplementary Datasets for "Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints". The deposition contains training/testing datasets used in the article.</p>
MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
<p>Cold-water corals build up reef structures or coral gardens and play an important role for many organisms in the deep sea. Climate change, deep-sea mining, and bottom trawling are severely compromising these ecosystems, making it all the more important to document the diversity, distribution, and impacts on corals. This goes hand in hand with species identification, which is morphologically and genetically challenging for Hexa- and Octocorallia. Morphological variation and slowly evolving molecular markers both contribute to the difficulty of species identification. In this study, a fast and cheap species delimitation tool for Octocorallia and Scleractinia of the Northeast Atlantic was tested based on 49 specimens. Two nuclear markers (ITS2 and 28S rDNA) and two mitochondrial markers (COI and mtMutS) were sequenced. The sequences formed the basis of a reference library for comparison to the results of species delimitation based on proteomic analysis using the MALDI-TOF MS method. The genetic methods were able to distinguish 17 of 18 presumed species. The MALDI-TOF MS method was able to distinguish 7 species. Species that could not be distinguished from one another still achieved good signals but were not represented by enough specimens for comparison. Therefore, it is predicted that with an extensive reference library of proteome spectra for Scleractinia and Octocorallia, MALDI-TOF MS may provide a rapid and cost-effective alternative for species discrimination in corals.</p>
Data from: Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone
<p><span>The Clarion Clipperton Fracture Zone (CCZ) is a vast deep-sea region harboring a highly diverse benthic fauna, which will be affected by potential future deep-sea mining of metal-rich polymetallic nodules. Despite the need for conservation plans and monitoring strategies in this context, the majority of taxonomic groups remains scientifically undescribed. However, molecular rapid assessment methods such as DNA-barcoding and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) provide the potential to accelerate specimen identification and biodiversity assessment significantly in the deep-sea areas. In this study, we successfully applied both methods to investigate the diversity of meiobenthic copepods in the eastern CCZ, including the first application of MALDI-TOF MS for the identification of these deep-sea organisms. Comparing several different species delimitation tools for both datasets, we found that biodiversity values were very similar, with Pielou's Evenness varying between 0.97 and 0.99 in all datasets. Still, direct comparisons of species clusters revealed differences between all techniques and methods, which are likely caused by the high number of rare species being represented by only one specimen, despite our extensive dataset of more than 2000 specimens. Hence, we regard our study as a first approach toward setting up a reference library for mass spectrometry data of the CCZ in combination with DNA-barcodes. We conclude that proteome fingerprinting, as well as the more established DNA-barcoding, can be seen as a valuable tool for rapid biodiversity assessments in the future, even when no reference information is available.</span></p>
MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
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Data from: Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone
Open the record for dataset details and reuse information.
FIGURE 2 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 2. Strict consensus tree of more than 2600 most parsimonious trees from analysis of the combined plastid matK and rpl16 intron sequences. Tree length = 451 steps, CI = 0.89 and RI = 0.85. Bootstrap percentages (> 50%) are indicated above branches. Cardiocrinum giganteum and Notholirion thomsonianum are the outgroups. See also Table 2.
FIGURE 4 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 4. Principal coordinate analysis (PCO) of eleven populations of Fritillaria tubiformis s.l. analyzed for ten microsatellite loci. The first (PCO1) and the second (PCO2) axes explain 50.4% and 20.9% of total variation, respectively. Acronyms correspond to populations (see Table 1). The two genetic groups corresponding to the two subspecific taxa are circled.
FIGURE 1 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 1. Map of the Italian populations of F. tubiformis s.l. Populations belonging to var. burnatii are labelled with a star and those belonging to subsp. moggridgei with a solid circle. Most sampled populations are located at the boundary between Piedmont (P) and Liguria (L) (Italy). Insets show, top left, sampling sites numbered as for populations (see Table 1) and, top right, the position of the sampled area within the Alps.
Targeting DNA-methylation Fingerprints Linked to Ultra-Processed Foods Consumption to Prevent Non-communicable Diseases: the METHYL-UP Study
ClinicalTrials.gov study NCT05319327. IPD Sharing: NO. Countries: 1. Publications: 0.
EpiPanGI Dx: A cell-free DNA methylation fingerprint for the early detection of gastrointestinal cancers
GEO Series GSE149438. Homo sapiens. 300 samples. Type: Methylation profiling by high throughput sequencing.
A DNA Methylation Fingerprint of 1,628 Human Samples
GEO Series GSE28094. Homo sapiens. 1628 samples. Type: Methylation profiling by array.
Validation of the Accuracy of DNA Fingerprinting Using Polar Bodies and Embryonic Cells
ClinicalTrials.gov study NCT01219517. IPD Sharing: Not stated. Countries: 1. Publications: 0.
................................................................................................................................................. Fig. 4. DNA fingerprint analysis of the four new isolates and other Bartonella species by ERICPCR. Lanes: M, molecular mass markers; 1, negative control; 2, R1T; 3, R3; 4, R4; 5, R6; 6, Bartonella henselae; 7, Bartonella quintana; 8, Bartonella bacilliformis; 9, Bartonella elizabethae; 10, Bartonella clarridgeiae; 11, Bartonella alsatica; 12, Bartonella tribocorum; 13, Bartonella grahamii; 14, Bartonella doshiae; 15, Bartonella vinsonii spp. arupensis; 16, Bartonella vinsonii spp. berkhoffii; 17, Bartonella vinsonii spp. vinsonii; 18, Bartonella koehlerae. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 4. DNA fingerprint analysis of the four new isolates and other Bartonella species by ERICPCR. Lanes: M, molecular mass markers; 1, negative control; 2, R1T; 3, R3; 4, R4; 5, R6; 6, Bartonella henselae; 7, Bartonella quintana; 8, Bartonella bacilliformis; 9, Bartonella elizabethae; 10, Bartonella clarridgeiae; 11, Bartonella alsatica; 12, Bartonella tribocorum; 13, Bartonella grahamii; 14, Bartonella doshiae; 15, Bartonella vinsonii spp. arupensis; 16, Bartonella vinsonii spp. berkhoffii; 17, Bartonella vinsonii spp. vinsonii; 18, Bartonella koehlerae.
FIGURE 3 in Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex
FIGURE 3. Median-joining (MJ) network for the combined plastid DNA data set of Fritillaria tubiformis s.l. A. MJ network based on indel repeats at locus 4, 7, 8, 9, 10. Haplotypes (Ha, Hb1 and Hb2) are indicated by circles, the size of each circle being proportional to the observed frequency of each haplotype. B. MJ network for the combined plastid DNA data set of Fritillaria tubiformis s.l. based on all ten microsatellites. Median vectors are labelled mv1, mv2, mv3 and mv4. Number of changes required to explain transitions among haplotypes is indicated along the lines of the networks, except for connections that required only a single change. Information on type and number of repeat motifs contributing to the network is provided for the two main clusters (A and B) corresponding to var. burnatii and subsp. moggridgei.
DNA methylation fingerprint of a KDM5C loss-of-function mutation in patients with intellectual disability
GEO Series GSE108423. Homo sapiens. 21 samples. Type: Methylation profiling by genome tiling array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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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