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Figure 1 from: Hu C, Wang S, Huang B, Liu H, Xu L, Hu Z, Liu Y (2020) The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes. ZooKeys 925: 73-88. https://doi.org/10.3897/zookeys.925.47820
Figure 1 Mitochondrial genome map of the Scolopendra mutilans. Genes drawn inside the circle are transcribed clockwise, and those outside are counterclockwise. PCGs are shown as brown arrows, rRNA genes as green arrows, tRNA genes as pink arrows. The innermost circle shows the GC content. GC content is plotted as the deviation from the average value of the entire sequence.
Figure 3 from: Hu C, Wang S, Huang B, Liu H, Xu L, Hu Z, Liu Y (2020) The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes. ZooKeys 925: 73-88. https://doi.org/10.3897/zookeys.925.47820
Figure 3 Mitogenome synteny among eight centipede species. Synteny analyses were generated in Mauve 2.4.0. A total of six large homologous regions were identified among the eight mitogenomes, while the sizes and relative positions of the homologous fragments varied across the mitogenomes.
Sequence analysis of tumors from immunosuppressed patients
<pre><strong>Rationale</strong>: This repository contains the intermediate data produced in <a href="https://www.nature.com/articles/s41598-019-56240-1">Passaro et al 2019</a>. <strong>Background</strong>: The metagenomic investigations have unveiled the tight relationship between microbes, viruses and human health. In this scenario potentially oncogenic viruses may play a key role in promoting cancer development in immunosuppressed subjects. T he raw data mentioned in the paper are accessible in the *SRA* repository under the BioProject <strong><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA544407">PRJNA544407</a></strong>. <strong>Methods</strong>: A thoroughly description about the bioinformatic analysis performed in Passaro et al 2019 are accessible at <a href="https://github.com/bfosso/SDATA_bio_Desc">https://github.com/bfosso/SDATA_bio_Deschttps://github.com/bfosso/SDATA_bio_Desc</a>. </pre>
Simulated read data analysed in "Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph"
<p>Simulated read data analyzed in "Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph".</p> <p><strong>1) Human sequence data</strong></p> <p><strong>HO_chr11_50bp_sliding_window*fq.gz:</strong><br> All possible 50 bp reads overlapping chromosome 11 SNPs in the Human Origins dataset. Files with the word "alternate" in their filename carry the alternate allele, otherwise, they carry the reference allele. Deamination has been added into these simulated reads using gargammel (Renaud 2016) based on empirically estimated post-mortem damage in a dataset of 102 ancient genomes (Allentoft et al., 2015).</p> <p><strong>2) microbial data</strong></p> <p><strong>simulation_*_s.fq.gz:</strong><br> Simulated microbial read data from a set of microbial reference genomes identified in the ancient Clovis genome (Rasmussen 2014), using gargammel.</p>
Haploweb analysis of ITS sequences of Leiopathes glaberrima (Cnidaria: Antipatharia)
<p>This a reanalysis of the ITS sequences of <em>Leiopathes glaberrima</em> published in Ruiz-Ramos DV, Saunders M, Fisher CR, Baums IB (2015) Home bodies and wanderers: sympatric lineages of the deep-sea black coral <em>Leiopathes glaberrima</em>. PLoS ONE 10:e0138989 (https://doi.org/10.1371/journal.pone.0138989). I thank the authors for sharing with me the original chromatograms of their study.</p> <p>The chromatograms were assembled into contigs in Sequencher then scrutinized to detect double peaks (using the procedure outlined in Fontaneto D, Flot J-F, Tang CQ (2015) Guidelines for DNA taxonomy, with a focus on the meiofauna. Marine Biodiversity 45:433–451; https://doi.org/10.1007/s12526-015-0319-7). Of the 43 individuals sequenced, 22 were homozygous (or had double peaks so small or noisy that it was impossible to infer their second haplotype with certainty, in which case they were considered as homozygous); two had a single double peak each (in which case phasing them was trivial); one had two double peaks (with strong differences in peak heights allowing direct phasing); and the remaining 18 were length-variant heterozygotes (characterized by many double peaks) that were phased using Champuru (Flot J-F (2007) Champuru 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths. Molecular Ecology Notes 7:974–977; https://doi.org/10.1111/j.1471-8286.2007.01857.x; available online at http://jfflot.mnhn.fr/champuru/). The two alleles of heterozygous individuals were named by appending -a and -b to the names of the corresponding individuals.</p> <p>Sequences were aligned using MAFFT's E-INS-i mode (Katoh K, Rozewicki J, Yamada KD (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20:1160–1166; https://doi.org/10.1093/bib/bbx108; available online at https://mafft.cbrc.jp/alignment/server/) then the resulting FASTA alignment was turned into a haploweb (Flot J-F, Couloux A, Tillier S (2010) Haplowebs as a graphical tool for delimiting species: a revival of Doyle’s “field for recombination” approach and its application to the coral genus <em>Pocillopora</em> in Clipperton. BMC Evolutionary Biology 10:372; https://doi.org/10.1186/1471-2148-10-372) using HaplowebMaker (Spöri Y, Flot J (2020) HaplowebMaker and CoMa: two web tools to delimit species using haplowebs and conspecificity matrices. Methods in Ecology and Evolution; https://doi.org/10.1111/2041-210X.13454; available online at https://eeg-ebe.github.io/HaplowebMaker/).</p> <p>In the resulting haploweb all haplotypes are connected into a single field for recombination (FFR sensu Doyle JJ (1995) The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Systematic Botany 20:574–588; https://doi.org/10.2307/2419811), thereby supporting the authors' original conclusion that all the specimens they sequenced were conspecific.</p> <p>Included in this dataset are:</p> <p>- a zipped folder containing the original chromatograms communicated by the authors (Leiopathes_ITS_chromatograms.zip);</p> <p>- a Sequencher 4.1 project file containing the chromatograms assembled into contigs, cleaned and phased (Leiopathes_ITS_Sequencher.spf);</p> <p>- a FASTA alignment of the phased sequences obtained (Leiopathes_ITS_MAFFT-E-INS-i.fasta);</p> <p>- a HaplowebMaker project file (in JSON format) containing the results of the haploweb analysis (Leiopathes_ITS_JSON.HaplowebMaker);</p> <p>- and a PDF printout of the final haploweb (Leiopathes_ITS_haploweb.pdf).</p> <p> </p> <p> </p> <p> </p>
Supplementary material 3 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2a
Supplementary material 7 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2e
Supplementary material 8 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2f
Supplementary material 4 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2b
Supplementary material 6 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2d
Supplementary material 1 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Tables S1–S6
Figure 9 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 9 Box plots of a length (bases) and b GC (%) content of ITS1 and ITS2 sequences for each one of the main lineages (Clades/Clusters) of the genus Ganoderma. The size of each box represents 50% of the values, the black horizontal line within each box indicates the median, the 'x' represents the average value, the error bars represent interquartile ranges and circles indicate outliers.
Supplementary material 5 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2c
Figure 8 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 8 Box plots of aITS sequence similarity (%) and b genetic distances (p-values) within (intra) and between (inter) Ganoderma species for each one of the main lineages (Clades/Clusters) of the genus, as well as pairwise comparisons between selected species. The size of each box represents 50% of the values, the black horizontal line within each box indicates the median, the 'x' represents the average value, the error bars represent interquartile ranges and circles indicate outliers. The red-dotted horizontal line, transversing the plots, represents the value levels accepted in this study for proposing new phylogenetic species.
Figure 6 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 6 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clades B, C and D. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of the tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 5 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 5 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade A, Cluster A.3. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of the tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 7 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 7 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade E. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 4 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 4 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade A, Clusters A.1 and A.2. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of tree) and geographic origin of the respective material (the latter appears in different font colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 3 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 3 Summary tree of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2). Thick lines represent ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95. Clades and Clusters within the tree appear as presented in Table 1 and Suppl. material 1: Table S2. Species names correspond to those inferred in this study. Scale bar: 0.01 nucleotide substitutions per site.
Figure 2 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 2 Basidiomes of Ganoderma spp. amongst those collected and analysed in this study (specimens codes appear in parantheses; Suppl. material 1: Table S1) aG. lucidum (A1180) bG. carnosum (DD1243) cG. resinaceum (2012-0077) dG. adspersum (2010-0015) eG. applanatum (DD2119) fG. pfeifferi (DD2118).
ScienceDex guides
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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.