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19,342 results for “sequence”
Sequencing data for "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays"
<p>Illumina and Oxford Nanopore sequencing datasets (in FASTQ format) generated for the manuscript "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays." Paired-end Illumina MiSeq data are uploaded as two separate files ("r1" and "r2") for each passaged population. BAM files, filtered to exclude reads that did not align to K3L, are provided for passaged populations analyzed in the manuscript.</p>
FIGURE 6. Maximum likelihood tree constructed using COI sequences with GenBank accession numbers. Bootstrap support values were calculated with a rapid bootstrapping algorithm for 1000 in Branchinotogluma bipapillata n. sp., a new branchiate scale worm (Annelida: Polynoidae) from two hydrothermal fields on the Southwest Indian Ridge
FIGURE 6. Maximum likelihood tree constructed using COI sequences with GenBank accession numbers. Bootstrap support values were calculated with a rapid bootstrapping algorithm for 1000 replicates in Raxml, and only those higher than 50 were shown.
FIGURE 6 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 6. Distribution of the five species of the N. melanoleuca complex. A full list of voucher specimens beyond those included in multivariate analyses and Appendix 2 is available on request from the first author.
FIGURE 1 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 1. Maximum likelihood mitochondrial phylogeny of the Naja melanoleuca complex. Node support values indicate % bootstrap support; support values for the most distal nodes not shown. Country abbreviations: CAR = Central African Republic, DRC = Democratic Republic of Congo, KZN = KwaZulu-Natal Province, South Africa, RoC = Republic of Congo. Mitochondrial candidate species (CS) are shown in the same colours as in Figures 2–4. For specimen information see Appendix 1.
FIGURE 5 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 5. Naja (Boulengerina) guineensis sp. nov. Left and top right: holotype, MNHN 1921.0485, dorsal and ventral view and side view of head. Note extensive mottling of throat and anterior ventral side and limited posterior extent of lighter ventral markings. Bottom right: live adult specimen measuring approximately 200 cm total length, from Sekondi-Takoradi, Western Region, Ghana, displaying dark suffusion of throat and anterior venter (not preserved; photo L. Chirio).
FIGURE 4 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 4. Ordination of individual specimens and OTU centroids of four of the mitochondrially defined candidate species of the N. melanoleuca complex along the first two canonical variates. CS5-peroescobari was omitted due to the small available sample size. Canonical variates 1 and 2 account for 57.9 and 22.8% of total variance, respectively. Enlarged symbols indicate OTU centroids.
FIGURE 3 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 3. Ordination of individual specimens in a Principal Coordinates Analysis of standardised multilocus distances of PRLR and UBN1 scnDNA sequence data. (a) All specimens; (b) Analysis repeated under exclusion of CS2 and CS3.
FIGURE 8 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 8. Naja (Boulengerina) melanoleuca. Adult specimens from Yaoundé, Cameroon (left—photo J.-F. Trape) and Tsibilé, Gabon (right—photo L. Chirio). Note the diffuse but distinct hood mark that is often present in this species, and the combination of broad main bands and narrow accessory bands on the ventral side.
FIGURE 9 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 9. Naja (Boulengerina) subfulva. Variation in colour and pattern. Top left: specimen from Kakamega, western Kenya, illustrating the typically deep black and white specimens with strong facial markings from the periphery of Lake Victoria. Bottom left: specimen from Chuka, Mount Kenya, Kenya, illustrating an extreme of the brown forebody and reduced facial pigmentation typical of the species in much of its range. Photos W. Wüster, courtesy Royjan Taylor / Bio-Ken snake farm live collection, Watamu, Kenya. Right: specimen from Bamenda, Cameroon, representing the form described by Stucki-Stirn (1979) as Naja melanoleuca aurata. Note the indistinct ventral bands and the lack of accessory ventral bands, as is typical of this species. Photo J.-F. Trape.
FIGURE 7 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 7. Naja (Boulengerina) savannula sp. nov. Top row and bottom left: holotype, MNHN 2018.0002. Bottom right: live specimen from Kindia, Guinea, showing conspicuous, broad dorsal bands and ventral banding, including narrow accessory bands (not vouchered). Photos J.-F. Trape.
FIGURE 2 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 2. Haplotype networks for single copy nuclear loci. (a) PRLR; (b) UBN1. Small black circles indicate unsampled haplotypes.
THE INFLUENCE OF PITCH FEEDBACK ON LEARNING OF MOTOR-TIMING AND SEQUENCING: A PIANO STUDY WITH NOVICES
<p>These files contain values and conditions for each subject in csv format.</p>
Bamfiles DNA sequencing reads HCT strain Fo1A and Fo2A
<p>Reads obtained from DNA sequencing of two strains resulting from the horizontal chromosome transfer experiment described in [doi: 10.1038/nature08850] and submitted to ENA [PRJEB29294] . For each strains two paired-end libraries were generated, one with ifragment length of about 170 bp and one with fragmentlength of 500 bp. They were first mapped to the genome of Fo47, unmapped reads were subsequently mapped to the genome of Fol4287, as described in [doi: 10.1101/465070]. Putative PCR duplicates were removed using Picard tools and resulting bamfiles (one for the 170 fragment library and one for the 500 bp fragment library) were merged.</p> <p>These files are the resulting bamfiles.</p> <p>Fo1A_L170_L500.unmapped_to_Fo47illumina.Fol4287broad.bowtie2.sorted_dedup.bam (one chromosome: chr 14)</p> <p>Fo2A_L170_L500.unmapped_to_Fo47illumina.Fol4287broad.bowtie2.sorted_dedup.bam (two chromosomes: chr 14 + small chromosome)</p>
Fig. 4 in Pollen characters and DNA sequence data converge on a monophyletic genus Iresine (Amaranthaceae, Caryophyllales) and help to elucidate its species diversity
Fig. 4. Scanning electron photomicrographs of pollen grains from the Iresine clade (= Iresinoids). A, Iresine cassiniiformis (Borsch & al. 3792); B, Iresine type XXXIV (Borsch & al. 5412); C, Iresine rzedowskii (Borsch & al. 3793); D, Iresine ajuscana (Borsch & al. 5404); E, Iresine orientalis (Borsch & al. 5404); F, Iresine discolor (Purpus 3453); G, Magnification of aperture with details of mesoporium of pollen from the same plant; H, Iresine hartmanii (Tenorino 1864); I, Iresine type XXXIV (Borsch & al. 5390). — Scale = 10 µm apart from G where it is 4 µm.
Fig. 7. Scanning electron photomicrographs from the alternantheroid and gomphrenoid clades. A in Pollen characters and DNA sequence data converge on a monophyletic genus Iresine (Amaranthaceae, Caryophyllales) and help to elucidate its species diversity
Fig. 7. Scanning electron photomicrographs from the alternantheroid and gomphrenoid clades. A, Pedersenia cardenasii (Borsch & Ortuño 3504); B, Pedersenia sp. (Borsch & Ibisch 3532); C, Magnification of aperture and details of mesoporia of pollen from the same plant; D, Hebanthe occidentalis (Borsch & Ortuño 3512); E, Pfaffia dunaliana (Borsch & Ortuño 3756); F, Magnification of aperture and details of mesoporia of pollen from the same plant. — Scale = 10 µm apart from C where it is 4 µm.
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>
Dataset - Selection of cyanobacteria over green algae in a photo-sequencing batch bioreactor fed with wastewater
<p>The data set attached consists of an excel file where the data from the article “<strong>Selection of cyanobacteria over green algae in a photo-sequencing batch bioreactor fed with wastewater”</strong>, published in Science of the Total Environment (vol. 653, 25<sup>th</sup> February 2019, 485-495.) can be found, as well as the different equations and formulae that were used to obtain the published results.</p>
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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)
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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.