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Fig. 5. Scanning electron photomicrographs from the Iresine clade. A in Pollen characters and DNA sequence data converge on a monophyletic genus Iresine (Amaranthaceae, Caryophyllales) and help to elucidate its species diversity
Fig. 5. Scanning electron photomicrographs from the Iresine clade. A, Iresine hebanthoides (Borsch & al. 5415); B, Magnification of aperture and details of mesoporia of pollen from the same plant; C, Iresine sousae (Mendez Ton 7192, isotype B); D, Iresine nitens (Borsch & al. 3770); E, Magnification of aperture and details of mesoporia of pollen from the same plant; F, Iresine latifolia (Borsch & al. 3790); G, Magnification of aperture and details of mesoporia of pollen from the same plant; H, Iresine diffusa (Borsch & al. 3676); I, Irenella cysotricha (Asplund 16555). — Scale = 10 µm apart from B, E and G where it is 4 µm and I where it is 2 µm.
Fig. 6. Scanning electron photomicrographs from the Iresine clade. A in Pollen characters and DNA sequence data converge on a monophyletic genus Iresine (Amaranthaceae, Caryophyllales) and help to elucidate its species diversity
Fig. 6. Scanning electron photomicrographs from the Iresine clade. A, Iresine angustifolia (Zumaya & al. 81); B, Iresine nigra (Zumaya & al. 77); C, View from a different angle onto a pollen grain from the same plant; D, Iresine interrupta (Zumaya 62); E, Iresine borschii (Ventura 9443, paratype); F, Iresine arbuscula (Castillo s.n.). — Scale = 10 µm.
Fig. 1 in Pollen characters and DNA sequence data converge on a monophyletic genus Iresine (Amaranthaceae, Caryophyllales) and help to elucidate its species diversity
Fig. 1. Morphological diversity of Iresine. A, Synflorescence of I. interrupta (Borsch & al. 3789); B, Pistillate flowers at maturity and C, Staminate flowers of I. interrupta (Borsch & al. 3789); D, Upright woody stem of Iresine type XXXIV (Borsch & al. 5390); E, Inflorescence and F, Woody stem of I. nigra (S. Zumaya & al. 77); G, Part of synflorescence with staminate (Borsch & al. 5385) and H, Pistillate flowers of I. ajuscana (Borsch & al. 5367). — Photos: T. Borsch.
Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files)
<p>This repository contains raw sequencing data (FASTQ files) produced from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2") . Sequencing libraries were prepared following the latest version of the nanoCAGE protocol (Poulain et al., Methods Mol Biol. 2017;1543:57-109. doi: 10.1007/978-1-4939-6716-2_4). They respectively contain a mix of 24 ("NC_LIMMS") and 18 ("NC_LIMMS2") samples tagged by specific barcode sequences at the 5'-ends (see tables below). The tagmentation step included in the protocol was performed using an equimolar mix of 12 Nextera XT N-series index primers (N701 to N712), therefore "NNNNNNNN" was indicated as index sequence on the Illumina Sample Sheet for the demultiplexing (see tables below). Libraries were sequenced paired-end on Illumina MiSeq system with the MiSeq Reagent Kit v3 (150 cycles: 58 cycles used for READ1, 8 cycles used for the Index, and 84 cycles used for READ2). Genomic alignments (BED files) of paired-end reads on human genome assemblies hg19 and hg38 using the MOIRAI pipeline (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1017276.</p> <p> </p> <p><em><strong>"170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") :</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>1 iPSC_control_rep1 4 ACAGAT NNNNNNNN</p> <p>2 iPSC_control_rep2 24 ATCGTG NNNNNNNN</p> <p>3 iPSC_control_rep3 31 CACGAT NNNNNNNN</p> <p>4 S3P1_OK_rep1 36 CACTGA NNNNNNNN</p> <p>5 S3P1_OK_rep2 46 CTGACG NNNNNNNN</p> <p>6 S3P1_OK_rep3 63 GAGTGA NNNNNNNN</p> <p>7 S4P1_OK_rep1 79 GTATAC NNNNNNNN</p> <p>8 S4P1_OK_rep2 92 TCGAGC NNNNNNNN</p> <p>9 S4P1_OK_rep3 9 ACATGA NNNNNNNN</p> <p>10 S4P2_OK_rep1 21 ATCATA NNNNNNNN</p> <p>11 S4P2_OK_rep2 33 CACGTG NNNNNNNN</p> <p>12 S4P2_OK_rep3 45 CGATGA NNNNNNNN</p> <p>13 S1P1_rep1 57 GAGATA NNNNNNNN</p> <p>14 S1P1_rep2 69 GCTCTC NNNNNNNN</p> <p>15 S1P1_rep3 81 GTATGA NNNNNNNN</p> <p>16 S3P1_FAILED_rep1 93 TCGATA NNNNNNNN</p> <p>17 S3P1_FAILED_rep2 11 AGTAGC NNNNNNNN</p> <p>18 S3P1_FAILED_rep3 23 ATCGCA NNNNNNNN</p> <p>19 S4P1_FAILED_rep1 35 CACTCT NNNNNNNN</p> <p>20 S4P1_FAILED_rep2 47 CTGAGC NNNNNNNN</p> <p>21 S4P1_FAILED_rep3 59 GAGCGT NNNNNNNN</p> <p>22 S4P2_FAILED_rep1 71 GCTGCA NNNNNNNN</p> <p>23 S4P2_FAILED_rep2 83 TATAGC NNNNNNNN</p> <p>24 S4P2_FAILED_rep3 95 TCGCGT NNNNNNNN</p> <p> </p> <p><em><strong>"180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"):</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>25 PETRI_rep1 04 ACAGAT NNNNNNNN</p> <p>26 PETRI_rep2 24 ATCGTG NNNNNNNN</p> <p>27 PETRI_rep3 31 CACGAT NNNNNNNN</p> <p>28 BIOCHIP_E_rep1 6 CACTGA NNNNNNNN</p> <p>29 BIOCHIP_M_rep1 46 CTGACG NNNNNNNN</p> <p>30 BIOCHIP_S_rep1 63 GAGTGA NNNNNNNN</p> <p>31 BIOCHIP_E_rep2 79 GTATAC NNNNNNNN</p> <p>32 BIOCHIP_M_rep2 92 TCGAGC NNNNNNNN</p> <p>33 BIOCHIP_S_rep2 09 ACATGA NNNNNNNN</p> <p>34 BIOCHIP_E_rep3 21 ATCATA NNNNNNNN</p> <p>35 BIOCHIP_M_rep3 33 CACGTG NNNNNNNN</p> <p>36 BIOCHIP_S_rep3 45 CGATGA NNNNNNNN</p> <p>37 HEPATOCYTES_rep1 57 GAGATA NNNNNNNN</p> <p>38 HEPATOCYTES_rep2 69 GCTCTC NNNNNNNN</p> <p>39 iPSC_control_rep1-2 81 GTATGA NNNNNNNN</p> <p>40 BIOCHIP_E_rep2-2 93 TCGATA NNNNNNNN</p> <p>41 BIOCHIP_M_rep1-2 11 AGTAGC NNNNNNNN</p> <p>42 BIOCHIP_S_rep2-2 23 ATCGCA NNNNNNNN</p>
Supplementary material 2 from: Zhao Y, Liu X-z, Bai F-y (2019) Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data. MycoKeys 47: 75-95. https://doi.org/10.3897/mycokeys.47.29180
Supplementary material 2 from: Zhao Y, Liu X-z, Bai F-y (2019) Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data. MycoKeys 47: 75-95. https://doi.org/10.3897/mycokeys.47.29180
Supplementary material 1 from: Zhao Y, Liu X-z, Bai F-y (2019) Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data. MycoKeys 47: 75-95. https://doi.org/10.3897/mycokeys.47.29180
Supplementary material 1 from: Zhao Y, Liu X-z, Bai F-y (2019) Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data. MycoKeys 47: 75-95. https://doi.org/10.3897/mycokeys.47.29180
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7). in An integrative taxonomic revision of the genus Triphosa Stephens, 1829 (Geometridae: Larentiinae) in the Middle East and Central Asia, with description of two new species
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7).
FIGURE 7. Sparsorythus multilabeculatus, 7a in Description of nymphs and female subimago of Sparsorythus multilabeculatus Sroka & Soldán, 2008 (Ephemeroptera: Tricorythidae) associated with male imago based on DNA sequence data
FIGURE 7. Sparsorythus multilabeculatus, 7a. foreleg; 7b. midleg; 7c. hindleg; 7d. female cerci and paracercus; 7e. segment of female cerci; 7f. male cerci and paracercus; 7g. segment of female cerci. Scale bars: 0.5 mm (7a–7c); 0.1 mm (7d, 7f); 0.02 mm (7e, 7g).
FIGURE 2 in Description of nymphs and female subimago of Sparsorythus multilabeculatus Sroka & Soldán, 2008 (Ephemeroptera: Tricorythidae) associated with male imago based on DNA sequence data
FIGURE 2. Wang Tao waterfall, Thap Lan National Park, Khon Buri District, Nakhon Ratchasima Province, Thailand, where the specimens of Sparsorythus multilabeculatus were collected.
FIGURE 1 in Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data
FIGURE 1. Best ML tree retrieved after analysing 43 taxa of family Phytolaccaceae. The best fit model of evolution GTR+G+I. The tree rooted at Hilleria latifolia (Lee et al. 2013).
FIGURE 3. A–E in Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data
FIGURE 3. A–E: Rivina humilis L.var. bracteata; A) Habit (inset flowers); B) Infructescence; C) Bract; D) Fruit; E) Seed; F–J: Rivina humilis L. var. humilis; F) Habit (inset flower); G) Infructescence; H) Bract; I) Fruit; J) Seed; K–O: Rivina bengalensis S. C. Srivastava et T. K. Paul; K) Habit (inset flowers); L) Infructescence; M) Bract; N) Fruit; O) Seed.
FIGURE 2 in Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data
FIGURE 2. Majority rule consensus tree from the BI analysis of the "total evidence" dataset from morphological and molecular data. Black lines represent the branches that remained identical in the strict consensus tree of the MP analysis. Grey lines represent branches obtained only in the BI analysis. Numbers in the nodes correspond to posterior probabilities and bootstrap values (PP/BT); dashes (-) represent low (<50%) or no BT support.
FIGURE 1 in Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data
FIGURE 1. Comparison of the phylogenetic hypothesis provided by the independent morphological and molecular datasets. Species of Ronnbergia are highlighted in red. A. Strict consensus of the four most parsimonious trees from the MP analysis of morphological data. Numbers in the nodes correspond to bootstrap values. B. Majority rule consensus tree from the BI analysis of the molecular dataset. Numbers in the nodes correspond to posterior probabilities and bootstrap values (PP/BT); dashes (-) represent low (<50%) or no BT support.
FIGURE 3 in Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data
FIGURE 3. Geographic distribution of the three clades containing species of Ronnbergia. Data points were obtained from the Global Biodiversity Information Facility—GBIF (www.gbif.org).
FIGURE 5 in Senecio kumaonensis (Asteraceae, Senecioneae) is a Synotis based on evidence from karyology and nuclear ITS/ETS sequence data
FIGURE 5. Specimens of Synotis penninervis (= Senecio kumaonensis). A. China, Xizang, Yadong, L. Wang & T. J. Tong 1352 (IBSC). B. China, Xizang, Gyirong, L. Wang & T. J. Tong 1373 (IBSC).
FIGURE 4 in Senecio kumaonensis (Asteraceae, Senecioneae) is a Synotis based on evidence from karyology and nuclear ITS/ETS sequence data
FIGURE 4. Cladogram inferred from combined ITS/ETS dataset using Bayesian inference (BI) method. Probabilities (> 0.70) are placed under branches, bootstrap support (> 50%) above branches. Open rectangles indicate the phylogenetic position of Synotis. The solid triangle indicates the phylogenetic position of Synotis penninervis (= Senecio kumaonensis).
FIGURE 3 in Senecio kumaonensis (Asteraceae, Senecioneae) is a Synotis based on evidence from karyology and nuclear ITS/ETS sequence data
FIGURE 3. Mitotic metaphase chromosomes (A, C) and karyotypes (B, D) in two populations of Synotis penninervis (= Senecio kumaonensis) from Xizang, China, all same scale. A. Yadong population (L. Wang & T.J. Tong 1352), 2n = 40 (arrows indicate satellited chromosomes). B. Yadong population (L. Wang & T.J. Tong 1352), 2n = 20m + 14sm (2sat) + 6st. C. Gyirong population (L. Wang & T.J. Tong 1373), 2n = 40. D. Gyirong population (L. Wang & T.J. Tong 1373), 2n = 20m + 14sm + 6st.
FIGURE 2 in Senecio kumaonensis (Asteraceae, Senecioneae) is a Synotis based on evidence from karyology and nuclear ITS/ETS sequence data
FIGURE 2. Floral micromorphology (A, C: anther collars, both same scale; B, D: anther tissue endothecial cell wall thickenings, both same scale) in two populations of Synotis penninervis (= Senecio kumaonensis) from Xizang, China. A, B. Yadong population (L. Wang & T.J. Tong 1352). C, D. Gyirong population (L. Wang & T.J. Tong 1373).
FIGURE 1 in Senecio kumaonensis (Asteraceae, Senecioneae) is a Synotis based on evidence from karyology and nuclear ITS/ETS sequence data
FIGURE 1. Synotis penninervis (= Senecio kumaonensis) in the wild. A. Habitat. B. Habit. C. Leaf blade (left: adaxial surface; right: abaxial surface). D. Synflorescence. E. Capitula. F. Phyllaries. G. Florets. H. Achenes.
FIGURE 4 in Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.
FIGURE 4. Inocyclus psychotriae (NY 01102760, isolectotype). a. Herbarium material. b, c. Ascostromata on leaves. D. Squash mount of dark brown to black ascostroma. e, f. Hand section of ascostroma (Note: the peridium without apical cells). g–h. Asci with ascospores immersed in water. i. Asci with ascospores immersed in KOH. j–l. ascospores. Scale bars: b = 1 mm, c = 100 μm, d–f = 20 μm, g–l = 5 μm.
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.