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19,342 results for “Sequences”
Data from: "Rare earth elements sediment analysis tracing anthropogenic activities in the stratigraphic sequence of Alagankulam (India)"
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Single-cell sequencing data of human umbilical cord and placental mesenchymal stem cells
<p>Expression matrix of umbilical cord and placenta single-cell sequencing data from the same donor.Table1 is the umbilical cord and Table2 is the placenta.</p>
RNA sequencing of macrophages co-cultured with MSCs and RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCs
<p>RNA sequencing of macrophages co-cultured with MSCS Table 5</p> <p>RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCS Table 8</p>
Experimental data on "Sediment storage and fluvial sediment transport linkages across an experimental flood sequence"
<p>The repository contains data used in manuscript "Sediment storage and fluvial sediment transport linkages across an experimental flood sequence" by Hassan, Pierce, Chartrand. </p>
FIGURE 4 Deduced amino-acid sequences for the Gnrh2 in Differential expression of HPG-axis genes in autotetraploids derived from red crucian carp Carassius auratus red var., × blunt snout bream Megalobrama amblycephala,
FIGURE 4 Deduced amino-acid sequences for the Gnrh2 () and Lhr () genes in Carassius auratus red var. (RCC) and autotetraploid C. auratus red var. ♀ × Megalobrama amblycephala ♂ (4nRR)
Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts
<p><span>Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant phage SVs, and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Strikingly, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.</span></p>
Code for generating figures and analyzing amplicon sequencing of human mRNA and reporter mRNA targeted with type III-A CRISPR complex from Streptococcus thermophiles
<p>This dataset contains code for analyzing amplicon sequencing data and generating figures in the manuscript by Anna Nemudraia, Artem Nemudryi, and Blake Wiedenheft (2024), "Repair of CRISPR-guided RNA breaks enables site-specific RNA excision in human cells." </p> <p>Amplicon sequencing data has been deposited to NCBI Sequence Read Archive (SRA) under BioProject PRJNA1099688. The description of read files deposited to SRA can be found in the spreadsheet ./code_for_sequencing_data_analysis/SRA_read_files_description.xlsx</p> <p>The code for analyzing amplicon sequencing data can be found in the archive "code_for_sequencing_data_analysis.tar.gz." Output files from this analysis were used to generate figures. Figures were generated using the ggplot2 package in R and finalized in CorelDRAW.</p> <p>Code for generating figures can be found in the archive "code_for_generating_figures.tar.gz". </p> <p>Any questions or requests regarding the data or the code should be addressed to Dr. Artem Nemudryi at artem.nemudryi@gmail.com.</p>
Automatic message sequence chart creation from simulation run of the parametric colored Petri net model of the Chandy-Lamport algorithm with four processes
<p><span>The video shows the creation of the message sequence chart from a simulation run of the proposed parametric colored Petri net model of the Chandy-Lamport algorithm using the CPN tool with four constituting processes. The picture shows the resulting message sequence chart. </span></p> <p><strong><span>Message Sequence Chart of Parametric Model With 4 Processes via Automatic Simulation Run_SuppInfo.mp4</span></strong><span>: This video shows the automatic generation of a message sequence chart of the proposed parametric colored Petri net model of the Chandy-Lamport distributed global snapshot algorithm using the CPN tool version 4.0.0. The model's number of constituting processes is parametric and was set to four. The video was generated using the authors' updated CPN tool extension server. The automatic simulation run of the model has been used to create this video. The CPN tool randomly selects the enabled transition at each step in an automatic simulation run.</span></p> <p><strong><span>Picture of Message Sequence Chart of Parametric Model With 4 Processes_SuppInfo.png:</span></strong><span> This picture shows the automatically generated message sequence chart of the proposed parametric colored Petri net model of the Chandy-Lamport algorithm that is visible in the above video clip. The number of constituting processes was set to four. </span></p>
Figures 42–46 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 42–46: Chamberlainium occidentale tetrasporangial anatomy. (42) Vertical section through the outer thallus showing an early stage tetrasporangial conceptacle primordium with peripheral roof development (black arrowheads) and a protective layer of epithallial cells (e) (L 3986120). Scale bar = 50 μm. (43) Vertical section through the outer thallus showing a later stage tetrasporangial conceptacle primordium with peripheral roof development (black arrowheads) and tetrasporangial (t) initials arranged peripherally around a central columella (c). Note the persisting layer of protective epithallial cells (e) (UWC 93/220). Scale bar = 50 μm. (44) Vertical section through the outer thallus showing a maturing tetrasporangial conceptacle with peripheral roof development (black arrowheads) and tetrasporangial (t) initials, peripherally arranged around a central columella (c). Note the layer of protective epithallial cells (e) (UWC 93/220). Scale bar = 50 μm. (45) Vertical section through a mature, raised tetrasporangial conceptacle showing tetrasporangia (t) with stalk cells (white arrowheads), peripherally arranged around a well-defined central columella (C). Note, the sunken and unoccluded pore opening (white arrow) (UWC 93/220). Scale bar = 100 μm. (46) Magnified view of the pore canal of a mature tetrasporangial conceptacle showing terminal, elongate initials (black arrows) that project into the pore canal as papillae and the base of the pore canal sunken (black arrowheads) into the chamber with terminal, elongate initials near the base pointing downward. Note, the sunken and unoccluded pore opening (white arrow) (UWC 93/220). Scale bar = 20 μm.
Figures 36–41 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 36–41: Chamberlainium occidentale gametangial anatomy. (36) Vertical section through the outer thallus showing a spermatangial conceptacle primordium with peripheral roof development (black arrows) and simple spermatangial systems (black arrowheads) confined to the conceptacle floor. Note the protective layer of epithallial cells (white arrow) (L 3986120). Scale bar = 50 μm. (37) Vertical section through a mature, raised spermatangial conceptacle showing the mucilage plug (white arrowhead) that occludes the pore opening and simple, spermatangial systems (black arrowheads) confined to the conceptacle floor (UWC 15/56). Scale bar = 50 μm. (38) Magnified view through a mature spermatangial conceptacle showing the pore canal lined with terminal, elongate initials (black arrowheads) that project into the pore canal as papillae (UWC 15/56). Scale bar = 20 μm. (39) Magnified view of a mature carpogonial conceptacle with carpogonial branches comprising a single support cell (s), a hypogynous cell (h) with sterile cell (black arrowhead), and a carpogonium (c) extended into a trichogyne (black arrows) that may project out of the pore. Note that the pore canal is lined with terminal, elongate initials (white arrows) that project into the pore canal as papillae (L 3986120). Scale bar = 20 μm. (40) Vertical section through a mature carposporangial conceptacle showing a discontinuous central fusion cell (black arrowhead) with peripherally arranged gonimoblast filaments each terminating in a carposporangium (C) (L 3986120). Scale bar = 50 μm. (41) Magnified view of the floor of a carposporangial conceptacle showing a discontinuous central fusion cell (black arrowheads) bearing a peripherally arranged gonimoblast filament (1–6) terminating in a carposporangium (C). The remains of unfertilised carpogonial branches (black arrow) persist across the dorsal surface of the central fusion cell (L 3986120). Scale bar = 20 μm.
Figures 26–30 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 26–30: Chamberlainium glebosum tetrasporangial anatomy. (26) Vertical section through the outer thallus showing an early stage tetrasporangial conceptacle primordium with peripherally arranged tetrasporangial initials (black arrowheads) and a protective layer of epithallial cells (black arrow) (UWC 15/17). Scale bar = 50 μm. (27) Vertical section through the outer thallus showing a later stage tetrasporangial conceptacle primordium with peripheral roof development (black arrowheads) with a developing central columella (white arrowhead). Note the persisting layer of protective epithallial cells (black arrow) (UWC 15/17). Scale bar = 50 μm. (28) Vertical section through a maturing tetrasporangial conceptacle showing tetrasporangial initials (t) arranged peripherally around a central columella (between white arrowheads). Note the layer of protective epithallial cells (black arrow) being shed (L 3986123). Scale bar = 50 μm. (29) Vertical section through a mature, raised tetrasporangial conceptacle showing tetrasporangia (t) with stalk cells (white arrowheads), peripherally arranged around a well-defined central columella (C). Note the base of the pore canal sunken into the chamber with terminal, elongate initials near the base pointing downward (black arrowheads) (UWC 15/55). Scale bar = 100 μm. (30) Magnified view of the pore canal of a mature tetrasporangial conceptacle showing terminal, elongate initials (black arrows) that project into the pore canal as papillae and the base of the pore canal sunken (black arrowheads) into the chamber with terminal, elongate initials near the base pointing downward (UWC 15/55). Scale bar = 20 μm.
Figures 24–25 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 24–25: Vertical section through the outer thallus showing spermatangial conceptacle primordium with peripheral roof development (black arrows) and simple spermatangial systems (black arrowheads) confined to the conceptacle floor. Note the protective layer of epithallial cells (white arrow). Scale bar = 50 μm. Vertical section through the outer thallus showing a mature, raised spermatangial conceptacle with the mucilage plug (white arrow) that occludes the pore opening and simple, spermatangial systems (white arrowheads) confined to the conceptacle floor. Note that the pore canal is lined with terminal, elongate initials (black arrowheads) that project into the pore canal as papillae. Scale bar = 50 μm.
Figure 1 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figure 1: Map of South Africa (gray shade), with an inset of False Bay, showing the coastal provinces, the biogeographic marine provinces and the approximate locations of collecting sites (● = Chamberlainium capense, ■ = C. glebosum,: = C. occidentale).
Figures 7–11 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 7–11: Chamberlainium capense habit and vegetative anatomy. (7) Rock fragment showing holotype specimen (white arrow) (L 3986119, tetrasporangial). Scale bar = 20 mm. (8) Encrusting to variably lumpy and slightly protuberant, epilithic thalli showing crusts abutting and easily discernible. Scale bar = 10 mm. (9) Vertical section through the margin (black arrow) showing the monomerous thallus construction with plumose medulla (M) giving rise to cortical filaments (C) that terminate in a single layer of epithallial cells (black arrowhead) (UWC 16/17). Scale bar = 50 μm. (10) Vertical section of the inner thallus showing cell fusions (f) between adjacent medullary filaments (UWC 16/17). Scale bar = 20 μm. (11) Vertical section of the outer thallus showing a single layer of epithallial cells (e) subtended by a layer of subepithallial initials (i). Note the paired, bottle-shaped trichocytes (t) (UWC 16/24). Scale bar = 20 μm.
Figures 4–6 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 4–6: Habit photographs of Chamberlainium capense, C. glebosum and C. occidentale. (4) Chamberlainium capense is moderately thick to mostly lumpy and only slightly protuberant. Scale bar = 20 mm. (5) Chamberlainium glebosum is thick, very lumpy and highly protuberant. Scale bar = 20 mm. (6) Chamberlainium occidentale is morphologically highly variable, occurring as thin encrusting (smooth) to thick warty (mostly) to lumpy plants, and are only slightly protuberant. Scale bar = 30 mm.
Figures 15–18 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 15–18: Chamberlainium capense tetrasporangial anatomy. (15) Vertical section through the outer thallus showing a later stage tetrasporangial conceptacle primordium with peripheral roof development (black arrowheads) and tetrasporangial initials (t) arranged peripherally around a central columella (c). Note the persisting layer of protective epithallial cells (black arrow) (L 3986119). Scale bar = 50 μm. (16) Vertical section through a mature, raised tetrasporangial conceptacle showing tetrasporangia (t) with a stalk cell (black arrowhead), peripherally arranged around a well-defined central columella (C). Note the remains of a corona (white arrow) that surrounds the pore opening (L 3986119). Scale bar = 50 μm. (17) Vertical section through a mature raised tetrasporangial conceptacle showing tetrasporangia (t) with stalk cells (black arrowheads), appearing to be arranged across the chamber floor as the columella (c) has disintegrated. Note the absence of the corona (white arrow) (UWC 16/09). Scale bar = 50 μm. (18) Magnified view of the pore canal of a mature tetrasporangial conceptacle showing the base of the pore canal sunken (black arrowheads) into the chamber with terminal, elongate initials near the base pointing downward (black arrows) and the remains of a corona (white arrow) that surrounds and occludes the pore opening. (L 3986119). Scale bar = 20 μm.
Figures 12–14 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 12–14: Chamberlainium capense spermatangial anatomy (UWC 16/21). (12) Vertical section through the outer thallus showing a spermatangial conceptacle primordium with peripheral roof development (black arrows) and simple, spermatangial systems (black arrowheads) confined to the conceptacle floor. Note the protective layer of epithallial cells (white arrow). Scale bar = 50 μm. (13) Vertical section through a mature, raised spermatangial conceptacle showing the mucilage plug (white arrowhead) that occludes the pore opening and simple, spermatangial systems (black arrowheads) confined to the conceptacle floor. Scale bar = 50 μm. (14) Magnified view through a mature spermatangial conceptacle showing the mucilage plug (white arrowhead) that occludes the pore opening and simple, spermatangial systems (black arrowheads) confined to the conceptacle floor. Note that the pore canal is lined with terminal, elongate initials (black arrows) that project into the pore canal as papillae. Scale bar = 20 μm.
Figure 3 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figure 3: Bayesian inference tree based on rbcL sequences. Species with sequenced type/'topotype' material are highlighted in bold. Generitype species within Corallinales are identified by a star (+). Species names are followed by their GenBank accession number and their geographic location, including ocean basin where needed. Numbers in brackets, following the GenBank accession numbers, are the total number of identical sequences. Bootstrap support (BS) and Bayesian posterior probability (BPP) values are provided at branch nodes. BS and BPP values = 100 % and = 1 respectively, are denoted by an asterisk (*); BS and BPP values <75 % and <0.75 respectively. Atl = Atlantic Ocean, Ind = Indian Ocean, Med = Mediterranean, Pac = Pacific Ocean.
Figure 2 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figure 2: Maximum likelihood tree based on psbA sequences. Species with sequenced type/'topotype' material are highlighted in bold. Generitype species and molecular references for generitype species within the Corallinales are identified by a star (+). Species names are followed by their GenBank accession number and their geographic location, including ocean basin where needed. Numbers in brackets, following the GenBank accession numbers, are the total number of identical sequences. Bootstrap support (BS) and Bayesian posterior probability (BPP) values are provided at branch nodes. BS and BPP values = 100% and = 1 respectively, are denoted by an asterisk (*); BS and BPP values <75 % and <0.75 respectively, are not shown. Atl = Atlantic Ocean, Ind = Indian Ocean, Med = Mediterranean, Nam = Namibia, NZ = New Zealand, Pac = Pacific Ocean.
Next-Generation Sequencing Dataset of Adult Pilocytic Astrocytomas
<p>Next-Generation Sequencing Dataset of Adult Pilocytic Astrocytomas</p> <p>Pilocytic astrocytoma (PA) is a benign grade 1 glioma according to the World Health Organization (WHO), common in children but rare in adults, where it may have a worse prognosis. Pediatric PA is usually associated with dysregulation of the MAPK pathway, often involving BRAF alterations such as the KIAA1549::BRAF (K-B) fusion or the V600E mutation. This dataset contains molecular data of 28 cases of adult PA obtained by using gene-targeted next-generation sequencing (NGS).</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)
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.