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Figure 1 from: Darschnik S, Leese F, Weiss M, Weigand H (2019) When barcoding fails: development of diagnostic nuclear markers for the sibling caddisfly species Sericostoma personatum (Spence in Kirby & Spence, 1826) and Sericostoma flavicorne Schneider, 1845. ZooKeys 872: 57-68. https://doi.org/10.3897/zookeys.872.34278
Figure 1 Schematic overview of the different multiplex and single RFLP fingerprints for S. flavicorne (Sf) and S. personatum (Sp). Fragment lengths are given above/below bands. Red: EcoRV1, EcoRV5, NdeI4, NdeI8, and PvuII2; Green: EcoRV4, EcoRV2, NdeI1, NdeI5.
Supplementary material 2 from: Darschnik S, Leese F, Weiss M, Weigand H (2019) When barcoding fails: development of diagnostic nuclear markers for the sibling caddisfly species Sericostoma personatum (Spence in Kirby & Spence, 1826) and Sericostoma flavicorne Schneider, 1845. ZooKeys 872: 57-68. https://doi.org/10.3897/zookeys.872.34278
: Data type: molecular data
Supplementary material 1 from: Darschnik S, Leese F, Weiss M, Weigand H (2019) When barcoding fails: development of diagnostic nuclear markers for the sibling caddisfly species Sericostoma personatum (Spence in Kirby & Spence, 1826) and Sericostoma flavicorne Schneider, 1845. ZooKeys 872: 57-68. https://doi.org/10.3897/zookeys.872.34278
: Data type: molecular data
Supplementary material 2 from: Ahmed M, Back MA, Prior T, Karssen G, Lawson R, Adams I, Sapp M (2019) Metabarcoding of soil nematodes: the importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s). Metabarcoding and Metagenomics 3: e36408. https://doi.org/10.3897/mbmg.3.36408
: Data type: source code
Supplementary material 1 from: Ahmed M, Back MA, Prior T, Karssen G, Lawson R, Adams I, Sapp M (2019) Metabarcoding of soil nematodes: the importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s). Metabarcoding and Metagenomics 3: e36408. https://doi.org/10.3897/mbmg.3.36408
: Data type: species data
Figure 2 in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 2. HKY distance of cytochrome b vs. CHD-Z (left) and myoglobin vs. CHD-Z (right). The line represents the relationship of overall sequence divergences between two segments and indicates that the cytb and myo sequences are diverging faster than the CHD-Z gene sequence (cytb/CHD-Z = 1.41 and myo/CHD-Z = 1.15).
Figure 2 in Investigation of the effect of silymarin on oxidative DNA damage and inflammatory markers in ischemia/reperfusion injury following experimental testicular torsion/detorsion in rats
Figure 2. Testicular tissue, control group, negative Tnf-α expression (A). T 3 h / D 3 h group: very severe Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (B). T 3 h / D 24 h group: severe Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (C). T 3 h / D 3 h + silymarin group: medium level Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (D). T 3 h / D 24 h + silymarin group: mild Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (E). IHC-P, bar: 50 µm.
Figure 1 in Investigation of the effect of silymarin on oxidative DNA damage and inflammatory markers in ischemia/reperfusion injury following experimental testicular torsion/detorsion in rats
Figure 1. Testicular tissue, control group, normal histological view (A). T 3 h / D 3 h group: necrosis in spermatocytes (arrowheads); severe congestion in intertubular intervals (thick arrows); hemorrhage, thinning in the tubulus wall (B). T 3 h / D 24 h: necrosis in spermatocytes (arrowheads); severe edema in the intertubular space (stars); thinning of the tubulus wall (C). T 3 h / D 3 h + silymarin group: moderate edema in the intertubular intervals (star); congestion (thick arrow) (D). T 3 h / D 24 h + silymarin group: mild edema at intertubular intervals (star) (E); H and E, bar: 50 µm.
Figure 3 in Investigation of the effect of silymarin on oxidative DNA damage and inflammatory markers in ischemia/reperfusion injury following experimental testicular torsion/detorsion in rats
Figure 3. Testicular tissue, control group, negative 8-OHdG expression (A). T 3 h / D 3 h group: severe cytoplasmic 8-OHdG expression in spermatocytes (arrowheads) (B). T 3 h / D 24 h group: severe cytoplasmic 8-OHdG expression in spermatocytes (arrowheads) (C). T 3 h / D 3 h + silymarin group: moderate cytoplasmic 8-OHdG expression in spermatocytes (arrowheads) (D). T 3 h / D 24 h + silymarin group: mild cytoplasmic 8-OHdG expression in spermatocytes (E), IHC-P, bar: 50 µm.
Fig. 2 in Mitochondrial marker-based analyses provide new insights into role of coral reef ecosystems in molluscan speciation
Fig. 2 Maximum likelihood phylogenetic tree based on partial mitochondrial COI gene sequences
Supplementary Datasets for Decoding the genetic markers symphony in Parkinson's Disease
Open the record for dataset details and reuse information.
Fig. 3 in A new subfamily classification of the Citrus family (Rutaceae) based on six nuclear and plastid markers
Fig. 3. Ancestral state reconstruction for the characters leaf type, phyllotaxis, flower merosity, number of stamen whorls and carpel connation. See Fig. 2 for taxon names.
Data from: ALG11 – a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene
Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.
Data from: Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing
The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species. We first obtained and mapped NGS transcriptome sequencing reads from two of the distantly related Brassicaceae species, Cardamine hirsuta and Arabis alpina, onto the Arabidopsis thaliana reference genome, and then identified short conserved sequence motifs among the three species bioinformatically. From these, primer pairs to amplify coding regions (nuclear protein coding loci, NPCL) and exon-primed intron-crossing sequences (EPIC) were developed. We identified 2,334 universally applicable primer pairs, targeting 1,164 genes, which provide a large pool of markers as readily usable genomic resource that will help addressing novel questions in the Brassicaceae family. Testing a subset of the newly designed nuclear primer pairs revealed that a great majority yielded a single amplicon in all of the 30 investigated Brassicaceae taxa. Sequence analysis and phylogenetic reconstruction with a subset of these markers on different levels of phylogenetic divergence in the mustard family were compared with previous studies. The results corroborate the usefulness of the newly developed primer pairs, e.g., for phylogenetic analyses or population genetic studies. Thus, our method provides a cost-effective approach for designing nuclear loci across a broad range of taxa and is compatible with current NGS technologies.
Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.
Figure 7 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 7. Aedeagus dorsal, lateral and ventral views of Arsipoda rostrata Gómez-Zurita sp. nov.
Figure 5 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 5. Pronotum of Arsipoda geographica Gómez-Zurita sp. nov.
FIGURE 8 in Molecular and morphological diagnostic markers for the Himalayan Ips DeGeer species (Coleoptera: Curculionidae: Scolytinae)
FIGURE 8. Male declivity in I. schmutzenhoferi (Holzschuh, 1988).
FIGURE 6 in Molecular and morphological diagnostic markers for the Himalayan Ips DeGeer species (Coleoptera: Curculionidae: Scolytinae)
FIGURE 6. Front of head in I. schmutzenhoferi. FIGURE 7. Female declivity in I. schmutzenhoferi.
Figure 2 in Diet of the black rat (Rattus rattus) in a Canary laurel forest: species identification based on morphological markers and DNA sequences
Figure 2. Seed of Rubus bollei/palmensis found intact in rat dropping.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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
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.