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zenodo32/100

FIGURE 12 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 12. Pseudopicrocuma japonicum sp. nov., ovigerous female. A, maxilliped 3; B–F, pereopods 1–5; G, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 11 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 11. Pseudopicrocuma japonicum sp. nov., ovigerous female. A, lateral view; B, anterior portion of body, from above; C, antenna 1; D, antenna 2; E, right and left mandibles; F, labium; G, maxilla 1; H, maxilla 2; J, K, maxillipeds 1, 2.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 13 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 13. Pseudopicrocuma japonicum sp. nov., adult male. A, lateral view; B, anterior portion of body, from above; C, anterior portion of carapace, lateral view; D, antenna 1; E, antenna 2; F maxilliped 3; G–K, pereopods 1–5; Q, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 10 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 10. Pseudopicrocuma japonicum sp. nov., preparatory female. A, maxilliped 3; B–F, pereopods 1–5; G, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 9 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 9. Pseudopicrocuma japonicum sp. nov., preparatory female. A, lateral view; B, anterior portion of body, from above; C, anterolateral angle D, antenna 1; E, antenna 2; F, right and left mandibles; G, labium; H, maxilla 1; I, maxilla 2; J, K, maxillipeds 1, 2.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 8 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 8. Atlantocuma ojii sp. nov., adult male. A, lateral view; B, anterior portion of body, from above; C, anterior portion of carapace, lateral view; D, antenna 1; E, antenna 2; F maxilliped 3; G–K, pereopods 1–5; Q, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 7 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 7. Atlantocuma ojii sp. nov., ovigerous female. A, lateral view; B, anterior portion of body, from above; C, carapace, lateral view; D, antenna 1; E, right and left mandibles; F, maxilla 1; G, maxilla 2; H–J, maxillipeds 1–3; K–O, pereopods 1–5; Q, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 6 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 6. Atlantocuma ojii sp. nov., preparatory female. A–E, pereopods 2–5; F, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 2 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 2. Atlantocuma gamoi sp. nov., preparatory female. A–D, pereopods 2–5; E, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 5 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 5. Atlantocuma ojii sp. nov., preparatory female. A, lateral view; B, anterior portion of body, from above; C, carapace, lateral view; D, antenna 1; E, antenna 2; F, right and left mandibles; G, maxilla 1; H, maxilla 2; I–K, maxillipeds 1–3.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 4 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 4. Atlantocuma gamoi sp. nov., adult male. A, lateral view; B, anterior portion of body, from above; C, anterior portion of carapace, lateral view; D, sculpture of integument of carapace; E, antenna 1; F, antenna 2; G, maxilliped 3; H–L, pereopods 1–5; Q, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
zenodo32/100

FIGURE 3 in Two new species of Atlantocuma (Crustacea: Cumacea), and a new genus and species from Japan, Northwest Pacific, with observations on the degeneration of mouthparts in ovigerous females

FIGURE 3. Atlantocuma gamoi sp. nov., ovigerous female. A, lateral view; B, anterior portion of body, from above; C, anterior portion of carapace, lateral view; D, antenna 1; E, antenna 2; F, right and left mandibles; G, maxilla 1; H, maxilla 2; I–K, maxillipeds 1–3; L–P, pereopods 1–5; Q, uropod with pleonite 6.

opennotspecifiedDec 2012View details →
dryad32/100

Data for: Global frequency analyses of canine progressive rod-cone degeneration–progressive retinal atrophy and collie eye anomaly using commercial genetic testing data

<p>Hundreds of genetic variants associated with canine traits and disorders have been identified, with commercial tests offered. However, the geographic distributions and changes in allele and genotype frequencies over prolonged, continuous periods of time are lacking. This study utilized a large set of genotypes from dogs tested for the progressive rod-cone degeneration–progressive retinal atrophy (prcd-PRA) G&gt;A missense PRCD variant (n = 86,667) and the collie eye anomaly (CEA)-associated NHEJ1 deletion (n = 33,834) provided by the commercial genetic testing company (Optigen/Wisdom Panel, Mars Petcare Science &amp; Diagnostics). These data were analyzed using the chi-square goodness-of-fit test, time-trend graphical analysis, and regression modeling in order to evaluate how test results changed over time. The results span fifteen years, representing 82 countries and 67 breeds/breed mixes. Both diseases exhibited significant differences in genotype frequencies (p = 2.7 × 10−152 for prcd-PRA and 0.023 for CEA) with opposing graphical trends. Regression modeling showed time progression to significantly affect the odds of a dog being homozygous or heterozygous for either disease, as do variables including breed and breed popularity. This study shows that genetic testing informed breeding decisions to produce fewer affected dogs. However, the presence of dogs homozygous for the disease variant, especially for prcd-PRA, was still observed fourteen years after test availability, potentially due to crosses of unknown carriers. This suggests that genetic testing of dog populations should continue.</p>

opencc-zeroDec 2023View details →
zenodo32/100

Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza.

<p><span>The dataset contains all the original raw files for images, including protein and RNA blots, DNA and protein sequences used for phylogenetic trees, do plots&hellip;, and any other type of source data, sorted by figure and figure panel. Plasmids generated for this study have been deposited in Addgene. They are listed below together with previously existing plasmids obtained from Addgene and used in this study. NGS data has been deposited on NCBI SRA, accession numbers of datasets used in each figure are listed accordingly in this document. Ready-to-visualize using IGV software files of all NGS datasets together with the S. polyrhiza 9509 gene and TE annotations are also provided. &nbsp;The content of each file is:</span></p> <p><span>&nbsp;</span></p> <p><strong><span>FIGURE 3:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>3A</span></strong><span>: Picture of Spirodela polyrhiza (used as well in S19A, S26B, D).</span></p> <p><span>&nbsp;</span></p> <p><strong><span>FIGURE 5:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>5A:</span></strong><span> Western blot raw TIFF image files for the detection of H3K9me1, H3K9me2 and H3 in Arabidopsis and Spirodela.</span></p> <p><span>&nbsp;</span></p> <p><strong><span>FIGURE 7:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>7A:</span></strong><span> Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_cDNA in input and IP fractions from transient expression in <em>N. benthamiana</em>.</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>7D:</span></strong><span> Raw scan image files of <em>N. benthamiana</em> leaves infiltrated with RUBY or Scarlet hairpin (hpScarlet) and Northern blots raw TIFF image files for the detection of siRNAs produced by RUBY and hpScarlet transiently expressed in <em>N. benthamiana</em>.</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>7E:</span></strong><span> Raw scan image files of Spirodela cultures in dishes infiltrated with RUBY or Scarlet hairpin (hpScarlet) and Northern blots raw TIFF image files for the detection of siRNAs produced by RUBY and hpScarlet transiently expressed in Spirodela.</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S6:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm DRB proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S7:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm RDR proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S8:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm DCL proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S9:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm AGO proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S10:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>DNA sequence of the Spirodela (Sp9509) Chromosome 7 fragment containing the AGO5 cluster.</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S11:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm SHH proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S12:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm Snf2 remodelers proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S13:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm Class V SET-domain containing proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S14:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm DNA methyltransferase proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S15:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm RNA pol large subunit proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S16:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several angiosperm SPT5 and SPT5L proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S17:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Protein sequences, and their alignment, of several animal and plant Uhrf/VIM proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S18:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S18A_B:</span></strong><span> Protein sequences, and their alignment, of several angiosperm SUVH4 and SUVH5/6 proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S18C_D:</span></strong><span> Protein sequences, and their alignment, of several angiosperm ASI1 proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S19:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Picture of Arabidopsis (used as well in S26 A,C).</span></p> <p><strong><span>&nbsp;</span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S24:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S24C:</span></strong> <span>Raw TIFF image files of the coomassie staining of histone acid-extraction protein samples run on SDS-PAGE gel.</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S24D:</span></strong><span> Excel files with mass-spectrometry data used for quantification of histone modifications in Arabidopsis and Spirodela.</span></p> <p><span>&nbsp;</span></p> <p><strong><span>SUPPLEMENTAL FIGURE S27:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S27A:</span></strong> <span>Raw czi and TIFF image files of Arabidopsis interphase nuclei stained with DAPI.</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S27B:</span></strong> <span>Raw czi and TIFF image files of Spirodela interphase nuclei stained with DAPI.</span></p> <p><span>&nbsp;</span></p> <p><strong><span>SUPPLEMENTAL FIGURE S34:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>DNA sequence files (fasta) of TEs used to generate dot plots</span><span>.</span></p> <p><span>&nbsp;</span></p> <p><strong><span>SUPPLEMENTAL FIGURE S35:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S35A:</span></strong> <span>Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_gDNA in input and IP fractions from transient expression in <em>N. benthamiana</em>.</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S35B:</span></strong> <span>Intron-annotated genomic DNA sequences of At<em>AGO4 </em>and Sp<em>AGO4a</em> in GenBank (.gbk) format.</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S35C:</span></strong><span> Raw image file of EtBr staining of agarose gel electrophoresis of 5&rsquo;OH-RACE prior to gel excision and cloning.</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><strong><span>S35D:</span></strong> <span>Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_cDNA in input and IP fractions from transient expression in <em>N. benthamiana</em>.</span></p> <p><span>&nbsp;</span></p> <p><strong><span>SUPPLEMENTAL FIGURE S36:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>DNA sequence files (fasta) of TEs used to generate dot plots</span><span>.</span></p> <p><span>&nbsp;</span></p> <p><strong><span>SUPPLEMENTAL FIGURE S38:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Pictures of Spirodela during pretreatment, manual and vacuum agroinfiltration and RUBY transient expression</span><span>.</span></p> <p><span>&nbsp;</span></p> <p><strong><span>GENOME BROWSER TRACKS:</span></strong></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>The following Integrative Genomics Viewer browser (</span><a href="https://igv.org/"><span>https://igv.org</span></a><span>) tracks are provided:</span></p> <p><span>SPIRODELA</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela 9509 genome (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela gene annotations (V3.0)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela TE annotations (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela H3K9me1 as log2[H3K9me1/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela H3K9me2 as log2[H3K9me2/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela H3K27me3 as log2[H3K27me3/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela H3K4me3 as log2[H3K4me3/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela H3K9me1 as log2[H3K9me1/H3] for H3K27me1 (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela H3K9me2 as log2[H3K9me2/H3] ] for H3K27me1 (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela H3K27me3 as log2[H3K27me3/H3] ] for H3K27me1 (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela TraPR purified 21-nt small RNAs (+ strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela TraPR purified 21-nt small RNAs (- strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela TraPR purified 22-nt small RNAs (+ strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela TraPR purified 22-nt small RNAs (- strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela TraPR purified 24-nt small RNAs (+ strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela TraPR purified 24-nt small RNAs (- strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela Illumina RNA seq coverage (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela Illumina RNA seq reads (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela PacBio Iso-seq coverage (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Spirodela PacBio Iso-seq reads (this study)</span></p> <p><span>&nbsp;</span></p> <p><span>ARABIDOPSIS</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis Col-0 genome (TAIR10)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis gene annotations (TAIR10)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis TE annotations (TAIR10)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings H3K9me1 as log2[H3K9me1/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings H3K9me2 as log2[H3K9me2/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings H3K27me3 as log2[H3K27me3/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings H3K4me3 as log2[H3K4me3/H3] (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings TraPR purified 21-nt small RNAs (+ strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings TraPR purified 21-nt small RNAs (- strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings TraPR purified 22-nt small RNAs (+ strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings TraPR purified 22-nt small RNAs (- strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings TraPR purified 24-nt small RNAs (+ strand) (this study)</span></p> <p><span>&middot;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Arabidopsis seedlings TraPR purified 24-nt small RNAs (- strand) (this study)</span></p> <p><span>&nbsp;</span></p> <p><strong><span>NGS DATASETS:</span></strong></p> <p><span>&nbsp;</span></p> <p><span>All the NGS data generated for this study can be found under the SRA BioProject ID PRJNA1164696. &nbsp;The data was used to generate the following figure panels:</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Figures: 1A-H, 2A-F, 3A-E, 4A-H, 5D-J, 6A-G, 7B, 7F-H</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Supplemental Figures: S1, S3, S4, S19, S20, S22, S23, S26, S28, S29, S30, S31, S32, S33, S35, S36, S37, S38.</span></p> <p><span>&nbsp;</span></p> <p><span>Publicly available sequencing data (from indicated datasets) was used to generate the following figures:</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Figure 2A-F (Arabidopsis gene expression): GSM6892968</span></p> <p><span>&nbsp;</span></p> <p><strong><span>MASS SPECTROMETRY DATA:</span></strong></p> <p><span>&nbsp;</span></p> <p><span>The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD050443. Data was used to generate:</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>Supplemental Figure 24D</span></p> <p><span>&nbsp;</span></p> <p><strong><span>PLASMIDS:</span></strong></p> <p><span>&nbsp;</span></p> <p><span>The following plasmids generated in this study can be retrieved from Addgene under the following ID#:</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>p35S:FHA-AtAGO4_gDNA: #216838</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>p35S:FHA-SpAGO4a_gDNA: #216841</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>p35S::FHA-SpAGO4a_cDNA: #216842</span></p> <p><span>&nbsp;</span></p> <p><span>The following plasmids used in this study were retrieved from Addgene under the following ID#:</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>p35S:RUBY: #160908</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>pZmUbq:RUBY: #160909</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>p35S:GFP-GUS: #167122</span></p> <p><span>&nbsp;</span></p> <p><span>The following plasmids were a gift from Dr. Marco Incarbone (Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam 14476, Germany).</span></p> <p><span>-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span>pAtUBQ:hpScarlet</span></p>

opencc-by-4.0Nov 2024View details →
dryad32/100

Robust cone-mediated signaling persists late into rod photoreceptor degeneration

<p>Rod photoreceptor degeneration causes deterioration in the morphology and physiology of cone photoreceptors along with changes in retinal circuits. These changes could diminish visual signaling at cone-mediated light levels, thereby limiting the efficacy of treatments such as gene therapy for rescuing normal, cone-mediated vision.  However, the impact of progressive rod death on cone-mediated signaling remains unclear. A mouse model of rod degeneration was used to investigate the fidelity of retinal ganglion cell (RGC) signaling throughout disease progression. Despite clear deterioration of cone morphology with rod death, cone-mediated signaling among RGCs remained surprisingly robust: spatiotemporal receptive fields changed little and the mutual information between stimuli and spiking responses was relatively constant. This relative stability held until nearly all rods had died and cones had completely lost well-formed outer segments. Interestingly, RGC information rates were higher and more stable for natural movies than checkerboard noise as degeneration progressed. The main change in RGC responses with photoreceptor degeneration was a decrease in response gain. These results suggest that gene therapies for rod degenerative diseases are likely to successfully prolong cone-mediated vision even if there are changes to cone morphology and density.</p>

opencc-zeroOct 2022View details →
zenodo32/100

Few juveniles or males were collected. Only four males from groups 7, 8, 9, and 11, all in clade D, were included in the dataset. The male in Fig. 13E–H conforms to the general morphological description of males in Lobocriconema with an undifferentiated labial region, the absence of a stylet, a degenerate pharyngeal region, a FIGURE 7. SEM images of specimens representing clades D (A–H) and B (I). NID numbers are associated with unique specimens, all are females except image C. A) Lobocriconema sp., face view with conspicuous labial disc surrounded by irregular labial structure, Nine-Mile Prairie, Nebraska, NID 4533. B) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Big Thicket National Preserve, Texas, NID 4560. C) Lobocriconema sp., juvenile, head with visible submedian lobes, body scales with fine terminal projections, Spring Creek Prairie, Nebraska, NID 4514. D) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Nine-Mile Prairie, Nebraska, NID 4527 E) Lobocriconema sp., cephalic profile with protruding stylet, Nine-Mile Prairie, Nebraska, NID 4529. F) Lobocriconema sp., head profile lacking submedian lobes, Tunica Hills, Louisiana, NID 4574. G) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4533. H) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4526. I) Lobocriconema sp., face view lacking submedian lobes, Great Smoky Mountains National Park, Purchase Knob, NID 4570. in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions

Few juveniles or males were collected. Only four males from groups 7, 8, 9, and 11, all in clade D, were included in the dataset. The male in Fig. 13E–H conforms to the general morphological description of males in Lobocriconema with an undifferentiated labial region, the absence of a stylet, a degenerate pharyngeal region, a FIGURE 7. SEM images of specimens representing clades D (A–H) and B (I). NID numbers are associated with unique specimens, all are females except image C. A) Lobocriconema sp., face view with conspicuous labial disc surrounded by irregular labial structure, Nine-Mile Prairie, Nebraska, NID 4533. B) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Big Thicket National Preserve, Texas, NID 4560. C) Lobocriconema sp., juvenile, head with visible submedian lobes, body scales with fine terminal projections, Spring Creek Prairie, Nebraska, NID 4514. D) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Nine-Mile Prairie, Nebraska, NID 4527 E) Lobocriconema sp., cephalic profile with protruding stylet, Nine-Mile Prairie, Nebraska, NID 4529. F) Lobocriconema sp., head profile lacking submedian lobes, Tunica Hills, Louisiana, NID 4574. G) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4533. H) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4526. I) Lobocriconema sp., face view lacking submedian lobes, Great Smoky Mountains National Park, Purchase Knob, NID 4570.

opennotspecifiedMar 2016View details →
zenodo32/100

Figs 7–8 in Flight muscles degeneration, oogenesis and fat body in Lasius niger and Formica rufa queens (Hymenoptera: Formicidae)

Figs 7–8. Indirect flight muscles, gaster fat body and ovaries in four young queens of F. rufa: 7 — from left to right: dissected mesosoma; gaster without tergites; gaster without part of the fat body for two alates; 8 — the same anatomy as described in 7 for two single dealate queens; abbreviations in the text. Scales: 1 mm. Рис. 7–8. Крыловые мыШцы непрЯмого действиЯ, жировое тело и Яичники четырёх молодых самок F. rufa: 7 — слева-направо: вскрытаЯ меЗосома; брюШко беЗ тергитов; брюШком с удаленной частью жирового тела у двух крылатых самок, 8 — то же, у двух бескрылых одиночных самок; обоЗначениЯ в тексте. МасШтаб — 1 мм.

opennotspecifiedDec 2020View details →
zenodo32/100

Fig. 3 in Flight muscles degeneration, oogenesis and fat body in Lasius niger and Formica rufa queens (Hymenoptera: Formicidae)

Fig. 3. Stages of indirect flight muscles degeneration in Formica rufa queens. Lateral view of a dissected mesosoma. Arrows indicate transitions from stages without external signs of necrosis (0) to stages in which hystolysis of muscle fibers occur (Hi1, Hi2) and their replacement by columns of adipocytes (Ad1, Ad2); other abbreviations — in the text. Рис. 3. Стадии дегенерации крыловых мыШц непрЯмого действиЯ у самок F. rufa. ВскрытаЯ меЗосома, сбоку. Стрелками покаЗаны переходы от стадии беЗ проЯвлений некроЗа (0) до гистолиЗа мыШечных волокон (Hi1, Hi2) и их ЗамеЩениЯ колонками адипоцитов (Ad1, Ad2); остальные обоЗначениЯ — в тексте.

opennotspecifiedDec 2020View details →
zenodo32/100

Figs 4–6 in Flight muscles degeneration, oogenesis and fat body in Lasius niger and Formica rufa queens (Hymenoptera: Formicidae)

Figs 4–6. Indirect flight muscles, gaster fat body and ovaries in three young dealate queens of L. niger: 4–5 — from left to right, a dissected mesosoma from a lateral view, a dorsal view of gaster without tergites, gaster without part of fat body; 6 — from left to right, a dissected mesosoma from a lateral view, ovaries from dorsal and ventral view; abbreviation in the text. Scales: 1 mm. Рис. 4–6. Крыловые мыШцы непрЯмого действиЯ, жировое тело брюШка и Яичники трёх молодых бескрылых самок L. niger: 4– 5 — слева-направо, вскрытаЯ меЗосома, сбоку; вид на брюШко беЗ тергитов, сверху; то же — удалена часть жирового тела; 6 — слева- направо, вскрытаЯ меЗосома, сбоку; Яичники — сверху и сниЗу; обоЗначениЯ в тексте. МасШтаб — 1 мм.

opennotspecifiedDec 2020View details →
zenodo32/100

Figs 1–2 in Flight muscles degeneration, oogenesis and fat body in Lasius niger and Formica rufa queens (Hymenoptera: Formicidae)

Figs 1–2. Reproductive systems in queen and workers of red wood ants: 1 — polytrophic ovariole, ovaries and oviducts in queen [partly after Schwanwitsch, 1949 and Otto, 1962]; 2 — stages of ovarian development in workers of F. rufa [after Otto,1958]; J — initial stage of ovarie, E1–E3 and V — growth stages, R1, R2 — stages of resorption, D — stage of degeneration; other — in the text. Рис. 1–2. ПоловаЯ система самки и рабочих у рыжих лесных муравьёв: 1 — политрофическаЯ ЯйцеваЯ трубочка, Яичники и половые пути самки [частично по Schwanwitsch, 1949 и Otto, 1962]; 2 — стадии раЗвитиЯ Яичников у рабочих F. rufa [по Otto,1958]; J — начальнаЯ стадиЯ Яичника, E1–E3 и V — стадии роста Яичников, R1, R2 — стадии реЗобциии, D — стадии дегенерации; прочeе — в тексте

opennotspecifiedDec 2020View details →

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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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record