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Supplementary phylogenetic trees of Babesia bigemina based on partial sequences of both genes Rap-1a and gp45, with SH-aLRT support values (%), aBayes support, and ultrafast bootstrap support (%).
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Sanger sequencing of target and off-target genomic regions for gene-edited iPSC clones with SETBP1 genetic variants
<p>This data set includes chromatograms generated using sanger sequencing of targeted regions of genomic DNA from clonal iPSC lines. The iPSC lines include clones generated using CRISPR/Cas9 homology directed repair to introduce genetic variants into <em>SETBP1,</em> and their wild-type controls. Additional files have been included in the data set to link chromatogram (ab1) files to specific iPSC clones for genomic regions across the variant in <em>SETBP1 (</em>SETBP1 clones genetic variant sanger sequencing.xslx)<em> </em>and top<em> </em>off-target sites (SETBP1 clones off-target sanger sequencing.xlsx). </p>
Whole genome RNA-sequencing reveals modulation of genes related to brain disorders by Withania somnifera in human neuroblastoma SK-N-SH cells
<p>Table S1: Human reference genome based differential gene expression; Figure S1: Reactome Pathway (50 μg/mL_3h vs C_3h); Figure S2: Reactome Pathway (50 μg/mL_9h vs C_9h); Figure S3: Reactome pathway (100 μg/mL_3h vs C_3h); Figure S4: GO Dose comparison; Reactome pathway (100 μg/mL_3h vs 50 μg/mL_3h); Figure S5: GO Dose comparison; Reactome pathway (100 μg/mL_9h vs 50 μg/mL_9h); Figure S6: GO Time comparison; Reactome pathway (50 μg/mL_9h vs 50 μg/mL_3h); Figure S7: GO Time comparison; Reactome pathway (100 μg/mL_9h vs 100 μg/mL_3h); Table S2: Disease ontology analysis of 100 μg/mL_3h vs 50 μg/mL_3h WS-treated SK-N-SH cells; Table S3: Disease ontology analysis of 100 μg/mL_9h vs 50 μg/mL_9h WS-treated SK-N-SH cells; Table S4: Disease ontology analysis of 100 μg/mL_9h vs 100 μg/mL_3h WS-treated SK-N-SH cells.</p>
In-house sequence database of S.pn recombinant protein vaccine target-related genes
<p>In-house sequence database of S.pn recombinant protein vaccine target-related genes.</p>
FIGURE 1 in Phylogenetic relationships among the genera of the Penaeidae (Crustacea: Decapoda) revealed by mitochondrial 16S rRNA gene sequences
FIGURE 1. Morphological phylogeny of the penaeid genera proposed by (a) Kubo 1949, reconstructed from text (genera in brackets were not fully analyzed and '?' refers to uncertain relationship) and (b) Burkenroad 1983, reconstructed from key (mentioned by the author as "...a natural key down to the level of genus"), with Penaeini as Peneini, Parapenaeini as Parapeneini, Trachypenaeini as Trachypeneini, and Metapenaeus as Mangalura. *Considered to be the most primitive genus in the family.
FIGURE 2 in Phylogenetic relationships among the genera of the Penaeidae (Crustacea: Decapoda) revealed by mitochondrial 16S rRNA gene sequences
FIGURE 2. BIO-neighbor-joining (BIO-NJ) tree of Penaeidae based on partial mitochondrial 16S rRNA gene sequences. Numbers on branches indicate bootstrap values from BIO-NJ (normal text), maximum parsimony (in italics), maximum likelihood (in bold) analyses and posterior probability values from Bayesian (in italics bold) analyses. Bootstrap values below 50% are not shown. A, B, C refer to the three main clades in the tree. Parapenaeini, Trachypenaeini and Penaeini are the three groups as defined by Burkenroad (1983).
Figure 3 in Molecular cloning and sequence analysis of the gene encoding interleukin-6 of the giant panda (Ailuropoda melanoleuca)
Figure 3. Phylogenetic relationships of IL-6 sequences from seven species in Carnivora. (A) Neighbour-joining tree of IL-6 nucleotide sequences based on Kimura's 2-parameter distances. (B) Maximum-parsimony tree of IL-6 mature protein sequences.
Figure 1 in Molecular cloning and sequence analysis of the gene encoding interleukin-6 of the giant panda (Ailuropoda melanoleuca)
Figure 1. RT-PCR of giant panda IL-6. The expected, 700bp fragment of giant panda IL-6 cDNA was amplified.
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Shanxi province, China
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Shanxi province, China
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 3 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 3. Phylogeography of Gongylomorphus skinks in Mauritius based on 1102bp of combined mtDNA sequence data. Lower-case letters refer to collection localities in Fig. 1 and Table 1. Haplotype networks are drawn with the areas of circles proportional to number of individuals observed; dots represent unobserved haplotypes, and lines between them each represent a single nucleotide substitution. Filled circles represent samples collected from extant populations, and open circles samples from extinct ones.
FIGURE 2 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 2. Bayesian maximum likelihood tree for extinct and extant Gongylomorphus skinks and a range of outgroup taxa, based on 1473 bp of combined mitochondrial (12S rRNA, cytochrome b) and nuclear (c-mos) DNA sequence. Numbers adjacent to nodes indicate: Bayesian posterior probability/MP bootstrap support values for analyses conducted using all samples (top line, if present), and only a subset of samples with full-length sequence for all three genes (bottom or only line). Letters a-s indicate the sampling locality in Mauritius for each specimen (Fig. 1, Table 1). Letters in bold are specimens which were sequenced for all three genes. Letters suffixed by an * are specimens that represent extinct populations.
FIGURE 1 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 1. (A) Map of the west Indian Ocean showing the location of the Mascarene islands. (B) Mauritius showing collection localities for Gongylomorphus bojerii skinks used in the present study. (C) Mauritius showing collection localities for Gongylomorphus 'orange-tail' and G. fontenayi skinks used in the present study. * indicates extinct populations.
Figure 5 in Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence
Figure 5. Photomicrographs of morphogenesis in Pseudoamphisiella elongata sp. nov. after protargol impregnation. A, middle part of cell, ventral view, showing the oral primordium for both dividers, and the undifferentiated parental structures; B, ventral view, arrows indicate the primary frontoventral–transverse (FVT) anlagen; C, ventral view of an early divider, arrowheads and arrows mark the left and right marginal row anlagen, respectively; D, a slightly later stage, note the merging of the macronuclear nodules, the arrow indicates the disaggregating of the old undulating membranes; E, ventral view of a middle-stage divider, arrows indicate the two migratory cirri derived from the last FVT cirral anlagen; F, middle portion of cell, ventral view, arrows mark the left marginal row anlagen in the opisthe; G, ventral view, arrows denote two migratory cirri derived from the last FVT cirral anlagen; H–J, ventral views of three specimens at slightly differing middle stages, the arrows in (H) and (J) indicate two migratory cirri derived from the last FVT cirral anlagen. Scale bars: 15 Mm in A; 50 Mm in C.
Figure 4 in Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence
Figure 4. Pseudoamphisiella elongata sp. nov. in the middle and late stages of morphogenesis, after protargol impregnation. A, B, ventral and dorsal views of the same specimen in the middle stage, showing the development of cirri and the single macronuclear mass; C, D, ventral and dorsal views of a late divider (same specimen), arrows indicate the differentiation of the extra anlagen, and arrowheads show the single caudal cirrus that develops from the posterior end of each dorsal kinety; E, ventral view of a late divider, note the newly built cirri; F, G, ventral and dorsal views of a very late divider, arrows indicate the newly formed extra right marginal cirri. Abbreviations: MVR, midventral row; RMR, right marginal row; TC, transverse cirri; UMA, undulating membrane anlagen. Scale bar: 60 Mm.
Figure 7. A in Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence
Figure 7. A, small subunit (SSU) rRNA gene sequence of Pseudoamphisiella elongata sp. nov. aligned with the sequences of Pseudoamphisiella alveolata, Pseudoamphisiella lacazei, and Pseudoamphisiella quadrinucleata. The numbers above the lines indicate the nucleotide numbers. The differences in sequence lengths were compensated for by introducing alignment gaps (–) in the sequences. Matched sites are marked with dots. B, phylogenetic tree of SSU rRNA sequences showing the positions of Pseudoamphisiella found with maximum-likelihood (ML) analysis, applying the GTR+G+I model. Species sequenced in the present study are shown in bold type. The numbers near branches are ML bootstrap values/Bayesian inference (BI) posterior probability values. The scale bar corresponds to five substitutions per 100 nucleotide positions.
Figure 2 in Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence
Figure 2. Photomicrographs of Pseudoamphisiella elongata sp. nov. from life (A–H) and after protargol impregnation (I–N). A–D, ventral views of different individuals, arrows mark the pellicular alveolus; E, lateral view, the inset shows part of the cortex, and the arrowheads indicate the rod-shaped extrusomes; F, portion of cortex (dorsolateral view), arrows indicate the extrusomes; G, outline shape of a stationary individual; H, dorsal view of cortex, showing the polygonalshaped alveoli; I, dorsal view, arrows mark the dorsal kineties; J, caudal portion, the arrow indicates the caudal cirri; K, middle portion of cell, ventral view, the arrow marks the end of the right midventral row; L, posterior end of body, ventral view, the arrows indicate the two fine pretransverse cirri that can be easily overlooked; M, anterior part of body, ventral view, arrows indicate the frontal cirri; N, ventral infraciliature. Scale bars: 100 Mm in A, B; 50 Mm in C, D, G, H.
Figure 6 in Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence
Figure 6. Photomicrographs of morphogenesis in Pseudoamphisiella elongata sp. nov. after protargol impregnation. A, ventral view, the arrow indicates the extra anlage adjacent to the right marginal row anlage; B, dorsal view, arrows denote the dorsal kineties anlagen; C, ventral view of opisthe in late stage, the arrow marks two buccal cirri; D, ventral view, arrowheads denote the pretransverse cirri; E–K, ventral views of middle to late stage dividers, showing the migration of all ciliary organelles and the division of the macronuclei; L, ventral view of a reorganizer at a late stage. Scale bars: 25 Mm in A; 60 Mm in E.
Figure 1 in Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence
Figure 1. Morphology of Pseudoamphisiella elongata sp. nov. from living observation (A–E) and after protargol impregnation (F–G). A, ventral view of a typical individual; B, ventral view of a slimmer individual; C, ventral view, note the ingested pennate diatoms; D, E, portion of cortex (top and side view), showing the polygonal-shaped alveoli and the rod-shaped extrusomes (arrows); F, ventral view of infraciliature, arrowheads indicate two fine pretransverse cirri; G, dorsal view of the same specimen as shown in (F), showing the macronuclear nodules, micronuclei, and dorsal kineties. Abbreviations: CC, caudal cirri; DK, dorsal kineties; EM, endoral membrane; FC, frontal cirri; LMR, left marginal row; Ma, macronucleus; Mi, micronucleus; MVR, midventral row; PM, paroral membrane; RMR, right marginal row; TC, transverse cirri. Scale bars: 50 Mm in A, B, C, F, G; 10 Mm in E.
Figure 3 in Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa, Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence
Figure 3. Pseudoamphisiella elongata sp. nov. after protargol impregnation, showing early to middle stages of morphogenesis. A, ventral view of an early stage divider, note the oral primordium in the proter (arrow) and opisthe (double-arrowheads), arrowheads indicate the primary frontoventral–transverse (FVT) cirral anlagen; B, ventral view, showing the early stage, arrows indicate the primary right marginal row anlagen; C, ventral view of an early divider, arrow marks the FVT-anlagen, arrowheads indicate the right marginal row anlagen, the double-arrowheads show the left marginal row anlagen in the opisthe; D, E, ventral and dorsal views of the same individual, arrowheads in D and E indicate the right marginal row anlagen and dorsal kineties anlagen, respectively; F, a slightly late divider, arrowheads indicate the extra anlagen; G, middle-stage divider, showing the dorsal kineties anlagen (arrows), the left marginal row anlagen (double-arrowheads), two migratory cirri derived from the last FVT-streak (arrowheads), and the hook-like extra anlagen; the inset shows the macronuclear nodules, and arrows mark the micronuclei. DKA: dorsal kineties anlagen.
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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)
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.