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19,342 results for “Sequence”
Methylation-free E.coli nanopore sequencing (ONT R9.4.1) data set
<p>The data set consists of fast5 files divided into 5 zip files (fast5_[1-5].zip), a genome record (Ecoli_K12_MG1655.fasta), an Illumina assembly genome (illumina_contigs.fasta) and a fastq file from Guppy 5 (guppy_basecalled.fastq.gz). We sequenced the Ecoli non-methylated genomic DNA (D5016, Zymo Research) with an ONT MinION device. The sequencing libraries were prepared by fragmenting the genomic DNA using Covaris g-TUBE and a Ligation sequencing kit (SQK-LSK109, Oxford Nanopore) with Flow Cell chemistry R9.4.1. We also performed short-read Illumina sequencing on the same sample using the TruSeq PCR-free library preparation on the MiSeq sequencing platform (Illumina, USA), and constructed a draft assembly from the Illumina sequencing results using SPAdes v3.6.0. We also upload a reference genome directly obtained from the E.coli sample producer website. </p> <p>In addition, the data set contains two fastq files that produced by the Lokatt basecaller (lokatt_basecalled.fasta.gz) and local-trained Bonito basecaller (bonito_local_basecalled.fastq.gz ), respectively, which are used for benchmarking in the Lokatt basecaller paper.</p>
MLL3 ChIP sequencing in murine and human HCC cells
<p>Mutations in genes encoding components of chromatin modifying and remodeling complexes are among the most frequently observed somatic events in human cancers. For example, missense and nonsense mutations targeting the mixed lineage leukemia family member 3 (<em>MLL3</em>/<em>KMT2C</em>) histone methyltransferase occur in a range of solid tumors and heterozygous deletions encompassing <em>MLL3</em> occur in a subset of aggressive leukemias. Although <em>MLL3</em> loss can promote tumorigenesis in mice, the molecular targets and biological processes by which MLL3 suppresses tumorigenesis remain poorly characterized. Here we combined genetic, epigenomic, and animal modeling approaches to demonstrate that one of the mechanisms by which MLL3 links chromatin remodeling to tumor suppression is by co-activating the <em>Cdkn2a</em> tumor suppressor locus. Disruption of <em>Mll3</em> cooperates with <em>Myc</em> overexpression in the development of murine hepatocellular carcinoma (HCC), in which MLL3 binding to the <em>Cdkn2a</em> locus is blunted, resulting in reduced H3K4 methylation and low expression levels of the locus-encoded genes, <em>Ink4a</em> and <em>Arf</em>. Conversely, elevated <em>MLL3</em> expression increases its binding to the CDKN2A locus and co-activates gene transcription. Endogenous Mll3 restoration reverses these chromatin and transcriptional effects and triggers <em>Ink4a</em>/<em>Arf</em>-dependent apoptosis. Underscoring the human relevance of this epistasis, we found that genomic alterations in <em>MLL3</em> and <em>CDKN2A</em> display mutual exclusivity in human HCC samples. These results collectively point to a new mechanism for disrupting CDKN2A activity during cancer development and, in doing so, link MLL3 to an established tumor suppressor network.</p>
Combined Effects of Rotation and Age Spreads on Extended Main-Sequence Turn Offs - Isochrones and Stellar Tracks
<p>Theoretical isochrones and EEP stellar tracks featured in <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...887..199G/abstract">Gossage et al. 2019</a> (Combined Effects of Rotation and Age Spreads on Extended Main-Sequence Turn Offs). These 1D stellar evolution models are based on <a href="https://docs.mesastar.org/en/release-r22.11.1/">MESA</a> r7503, and utilize the same physical assumptions as in MIST v1.0 (<a href="https://ui.adsabs.harvard.edu/abs/2016ApJ...823..102C/abstract">Choi et al. 2016</a>).</p> <p>The models are described in <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a> and <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...887..199G/abstract">Gossage et al. 2019</a>\(^1\), but salient features include:</p> <ul> <li>Metallicities [Fe/H] = -0.45, -0.30, -0.15, 0.0, 0.15, 0.30, 0.45 (assuming <a href="https://ui.adsabs.harvard.edu/abs/2009ARA%26A..47..481A/abstract">Asplund et al. 2009</a> protosolar abundances \(\rm Z_{\odot}\) = 0.0142).</li> <li>Rotation rates from v/v<sub>crit </sub>= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 (initiated at ZAMS)</li> <li>Masses from 0.1 to 8 solar masses with spacings of: <ul> <li>\(\rm \Delta M = 0.05 M_{\odot}\) for \(\rm M < 1 M_{\odot}\)</li> <li>\(\rm \Delta M = 0.04 M_{\odot}\) for \(\rm 1 M_{\odot} \leq M < 2 M_{\odot}\)</li> <li>\(\rm \Delta M = 0.2 M_{\odot}\) for \(\rm 2 M_{\odot} \leq M \leq 8 M_{\odot}\)</li> </ul> </li> <li>Models are evolved up to the first thermal pulse.</li> </ul> <p><strong>File name convention:</strong> zip files, e.g., \(\texttt{MIST_v1.0_feh_p0.15_rotating_tracks.zip}\), contain theoretical models at a particular metallcity ([Fe/H] = 0.15 in this case), at all rotation rates and masses. The file \(\texttt{MIST_v1.0_feh_m0.15_rotating_tracks.zip}\) contains models at [Fe/H] = -0.15, and so on. \(\texttt{*_tracks.zip}\) contain EEP stellar track files and \(\texttt{*_isochrones.zip}\) files contain theoretical isochrone files, both in the same format as EEP track and theoretical isochrones found on the <a href="https://waps.cfa.harvard.edu/MIST/index.html">MIST website</a>. Zip files labeled, e.g.,\(\texttt{*_isochrones_FILTERSET.zip}\) contain observable isochrones, with synthetic photometry produced for a particular filter set (as on the <a href="https://waps.cfa.harvard.edu/MIST/model_grids.html">MIST packaged grids</a> site, which contains more information on the filter sets), computed without extinction (\(A_V=0\)). At the moment, filter sets for \(\texttt{UBVRIplus}\) (containing Gaia filters), \(\texttt{HST_WFC3}\), \(\texttt{HST_ACSWF}\), \(\texttt{HST_WFPC2}\), and \(\texttt{CFHTugriz}\) are included, but more can be added upon request\(^2\). </p> <p><strong>Notes:</strong></p> <p>\(^1\) These are the same models as featured in <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a>, but in that work, [Fe/H] = -0.60 and -0.75 were featured as well and only included models up to v/v<sub>crit </sub>= 0.6. We include these models from <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a> here as well. Models at [Fe/H] = -0.60 have been extended to v/v<sub>crit </sub>= 0.9, while [Fe/H] = -0.75 only includes up to the original v/v<sub>crit </sub>= 0.6.</p> <p>\(^2\) These tracks and isochrones may be converted into observable tracks and isochrones (w/ gravity darkening effects if desired) via Aaron Dotter's <a href="https://github.com/aarondotter/iso">iso code</a>.</p> <p>\(^3\) Although astroseismic \(\nu_{max}\) and \(\Delta \nu\) are included in the included history files, be aware that these are based on scaling relations reliant on solar values, assuming the Coriolis and centrifugal forces do not play a role. While an OK assumption for the Sun, this is less applicable models with rapid rotation and their values should not be trusted in such regimes.</p>
COVFlow: performing virus phylodynamics analyses from selected SARS-CoV-2 genome sequences
<p>This upload contains pipeline configuration files, output data, scripts and data identifiers (GISAID EPI_ISL_ID) required to reproduce the results of the article entitled "COVFlow: performing virus phylodynamics analyses from selected SARS-CoV-2 genome sequences".</p>
Demogaphic Reconstruction of the Western Sheep Expansion from Whole-Genome sequences
<p>Sheep (<em>Ovis aries</em>) were among the earliest livestock, domesticated in the Fertile Crescent about 12000-10000 years ago with a nearly worldwide distribution today. Most of our knowledge about the timing of their expansion stems from archaeological data but it is unclear how the genetic diversity of modern sheep fits with these dates. We used whole-genome sequencing data of 63 domestic breeds and their wild relatives, the Asiatic mouflon (<em>O. gmelini</em>), to explore the demographic history of sheep. <br> On the global scale, our analysis revealed geographic structuring among breeds with unidirectional recent gene flow from domestics into Asiatic mouflons. We then selected four representative breeds from Spain, Morocco, the UK and Iran to build a comprehensive demographic model of the western sheep expansion.<br> We inferred a single domestication event around 9,000 years ago, slightly later than archaeological evidence suggests which might reflect uncertainties in the generation time used for these estimates. The westward expansion is dated to approximately 5,000 years ago, later than the original Neolithic expansion of sheep and approximately matching the Secondary Product Revolution associated with woolly sheep. We see some signals of recent gene flow from an ancestral population into southern European breeds which could reflect admixture with feral European mouflon. Furthermore, our results indicate that many breeds experienced a reduction of their effective population size during the last centuries, probably associated with the breed development.<br> Our study provides insights into the complex demographic history of western Eurasian sheep, highlighting interactions between breeds and their wild counterparts.</p>
Data from: Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation between Mimulus luteus var. luteus and M. l. variegatus
<p><span>Biologists have long been interested in understanding genetic constraints on the evolution of development. For example, noncoding changes in a gene might be favored relative to coding changes due to being less constrained by pleiotropic effects. Here we evaluate the importance of coding-sequence changes to the recent evolution of a novel anthocyanin pigmentation trait in the monkeyflower genus <em>Mimulus</em>. The magenta-flowered <em>Mimulus</em> <em>luteus</em> var. <em>variegatus</em> recently gained petal lobe anthocyanin pigmentation via a single-locus Mendelian difference from its sister taxon, the yellow-flowered <em>M. l. luteus</em>. Previous work showed that the differentially expressed transcription factor gene <em>MYB5a</em>/<em>NEGAN</em> is the single causal gene. However, it was not clear whether <em>MYB5a</em> coding-sequence evolution (in addition to the observed patterns of differential expression) might also have contributed to increased anthocyanin production in <em>M. l. variegatus</em>. Quantitative image analysis of tobacco leaves, transfected with <em>MYB5a</em> coding sequence from each taxon, revealed robust anthocyanin production driven by both alleles. Counter to expectations, significantly higher anthocyanin production was driven by the allele from the low-anthocyanin <em>M. l. luteus.</em> Together with previously-published expression studies, this supports the hypothesis that petal pigment in <em>M. l. variegatus</em> was not gained by protein-coding changes, but instead solely via non-coding cis-regulatory evolution. Finally, while constructing the transgenes needed for this experiment, we unexpectedly discovered two sites in <em>MYB5a</em> that appear to be post-transcriptionally edited – a phenomenon that has been rarely reported, and even less often explored, for nuclear-encoded plant mRNAs.</span></p>
Data for publication "Measuring the environment of a Cs qubit with dynamical decoupling sequences"
<p>Data sets as plotted in the preprint "Measuring the environment of a Cs qubit with dynamical decoupling sequences" are uploaded.<br> The zip file "data" contains a folder for each figure in the preprint (named after the figure). Each folder contains the data for all graphs in the respective figure.</p>
Figure 2 in Mitochondrial 12S rRNA sequences support the existence of a third species of freshwater blackfish (Percicthyidae: Gadopsis) from south-eastern Australia
Figure 2. Phylogenetic trees, using the PAUP software package (Swofford, 1998). A, Maximum parsimony, using a full exhaustive search with 1000 bootstrap replicates. B, Distance analysis, using the neighbour-joining option, bootstrap replicates set at 1000. C, Maximum likelihood, using the Tamura-Nei model with 100 bootstrap replicates.
The sequence of motions of water and sediment in a single plunging breaker on a sandy beach
<p><em>In memoriam Gerard Pichel (1948-2023), a champion of expert, lay, and tacit knowledge</em></p> <p> </p> <p>This deposit, having <a href="https://doi.org/10.5281/zenodo.7601924" target="_blank" rel="noopener">10.5281/zenodo.7601924</a> as entry DOI, distributes the sequence of images of a single breaker plunging onto a sandy beach on a windless day. This cover page gives an extended commentary. The still frames have been extracted from an <a href="https://commons.wikimedia.org/wiki/File:P%C3%A1jara_-_Morro_Jable_-_Playa_del_Matorral_(0)_09.ogv" target="_blank" rel="noopener">impromptu video in the Wikimedia Commons</a> (Vincentz 2013) showing remarkably clearly a shoaling wave that steepens suddenly, grows into a sequence of narrowly spaced plunging breakers, and dissolves in spray and foam. Also clearly visible are the sand stirred and suspended in the foreshore and, upon close inspection, that entrained within the curling wave.</p> <h3>Deposit content</h3> <ul> <li>A redistribution of the unprocessed <a href="https://commons.wikimedia.org/wiki/File:P%C3%A1jara_-_Morro_Jable_-_Playa_del_Matorral_(0)_09.ogv" target="_blank" rel="noopener">source video</a> (Vincentz 2013);</li> <li>Three hundred ninety distortion-free colour pictures of 1240x670 pixels, in PNG lossless format, 40ms apart (25 fps);</li> <li>Four videos reassembling these processed pictures at different playback speeds (as fast as the physical time, and two-, four- and eightfold slower); they can be viewed in this <a href="https://youtube.com/playlist?list=PLV5KQfKi7EFge-1gDEMyPGOlNCEQ9QDNM&feature=shared" target="_blank" rel="noopener">YouTube playlist</a>;</li> <li>The script used for image extraction and manipulation.</li> </ul> <h3>Motivation</h3> <p>These images may have informative, didactic and aesthetic value for those intrigued by shore dynamics and wave mechanics, whether initiated or uninitiated. Although the recording concerns a single wave event, even experts risk becoming the least alert to the intricacies of reality. By slow degrees, clinging to unavoidable simplifications may turn expertise into complacency and blunt the genuine appreciation of ground truth (<a href="https://doi.org/10.1057/jos.2008.7" target="_blank" rel="noopener">Salt 2008</a>). <br>After all, all research approaches suffer from limitations that make it difficult to distil widely applicable knowledge from complex evidence. For example, experiments are constrained by geometry and by the scaling laws of sand grains; simulations, by modelling three-phase turbulent interactions with very short scales; and parametrizations of field campaigns, by trading off general against locally relevant information. Every avenue of investigation thus leaves us with something to desire.<br>On the upside, appreciating the challenges in foreshore science and engineering does not necessarily require continuous first-hand experience on the beach. It is therefore hoped that this dataset stimulates appreciation, contemplation, investigation and/or study.</p> <h3>Dataset licensing</h3> <p>(Re-)using the material of this deposit is permitted free of charge under a licence<strong> <a href="https://creativecommons.org/licenses/by-sa/4.0/" target="_blank" rel="noopener">CC BY-SA (attribution and share-alike) 4.0</a></strong>. This is in keeping with the CC <a href="https://wiki.creativecommons.org/wiki/ShareAlike_compatibility" target="_blank" rel="noopener">compatibility conditions</a> and the share-alike restriction from the original video of Vincentz 2013, published under a licence <a href="https://creativecommons.org/licenses/by-sa/3.0/deed.en" target="_blank" rel="noopener"><strong>CC BY-SA 3.0</strong></a>. <br>See §4.1 about how to cite this work.</p> <h3>Dataset description</h3> <p>The ensuing sections describe:</p> <ol> <li>the qualitative physics;</li> <li>the procedure of image extraction and manipulation;</li> <li>the content and arrangement of the dataset;</li> <li>the citation format, version information, and vision for this deposit.</li> </ol> <h1>1. Physical description</h1> <p>An abridged version of this section is also available from the <a href="https://www.coastalwiki.org/wiki/Plunging_wave_in_slow_motion" target="_blank" rel="noopener">Coastal Wiki</a>. </p> <h2>1.1 Location</h2> <p>Vincentz (2013) places the video location at the sandy beach <a href="https://es.wikipedia.org/wiki/Playa_del_Matorral" target="_blank" rel="noopener">Playa del Matorral</a>. This is in the locality <a href="https://en.wikipedia.org/wiki/Morro_Jable" target="_blank" rel="noopener">Morro Jable</a> (<a href="https://www.openstreetmap.org/?mlat=28.050897&mlon=-14.352003" target="_blank" rel="noopener">28.050897°, -14.352003°</a>; municipality of <a href="https://en.wikipedia.org/wiki/P%C3%A1jara" target="_blank" rel="noopener">Pájara</a>) in the island of Fuerteventura, Canary Islands, Spain. The precise geolocation of the images is unknown. The Playa del Matorral faces SSW and SE and thus, roughly speaking, the African coast. The region is tidal: the water-level excursion at the nearby Puerto del Rosario is reported to be 2.3 m at springs and 1.6 m at neaps (NGA 2022, p.258). It is hence conceivable but not demonstrable that the flood tide may have contributed to the wave recorded in the video.</p> <p>The <a href="https://emodnet.ec.europa.eu/geoviewer/#?layers=12996:1:0,12997:1:0,12995:1:1,13005:1:1&basemap=ebwbl&active=12997&bounds=-14.480427655259211,27.951455702530858,-14.218911276738245,28.10884469989302&filters=" target="_blank" rel="noopener">EMODnet bathymetry</a> shows that seabed declines fairly steeply, approximately down to -500 m within 2 km or less from the mean sea level line. The development of a plunging breaker indicates in itself that the beach is behaving as a reflective one. Qualitatively, the closeness to the shore of the breaking line, the narrow shoreface, and the collision of backwash and incoming waves are additional indicators of a steep beach profile (Komar 1998). If present at all, sand bars do not appear to affect the breaking process. Inferences on the local beach profile seem purely speculative, although the particular profile may cause the peculiar behaviour of this one breaker, for example because of a submerged step close to the plunge point. In a steady beach configuration, these plunging waves must bring ashore sufficient sediment to compensate for the offshore transport down the steep slope.</p> <h2>1.2 Calendar</h2> <p>The <a href="https://commons.wikimedia.org/wiki/File:P%C3%A1jara_-_Morro_Jable_-_Playa_del_Matorral_(0)_09.ogv" target="_blank" rel="noopener">record at Wikimedia Commons</a> only attributes the video the date ‘11 February 2013’. The time stamp of the video file is '16 October 2013'. It is then likely that the former date indicates when the video has been taken. Since the Playa del Matorral faces both east and west, the skylight illumination does not provide clues as for the time of the day. The stage of the tide cannot be estimated either. All in all, the precise time and date are of little relevance for the small-scale development of the single wave seen in the video.</p> <h2>1.3 Description of motion</h2> <p>Contemplated in its entirety, the recording conveys the dramatic impression of a prototypical plunging wave dissolving explosively in spray and foam on a natural beach. The onset and development of breakers in the shoreface awes us because of the rapidity, dynamic range, and chaotic and cyclic behaviours embedded in their motion.</p> <p>The scales of motion interleaved in the the mixture of water, sand and air within such a sudden and rapid event become clearer thanks to the still frames and to the slowed-down videos. Although inferences about features out of view remain somehow speculative, the qualitative details in the recording reveal distinctive features and stages of development:</p> <ol> <li>Waves shoal with long arrival times. A single episode of breaking occurs as if in the isolation of a solitary wave, discounting that here the backrush of each wave feedbacks into the next wave's steepening. Extrapolating the evidence from the recording, this breaking might actually mark a small-amplitude swell, or edge wave, with a period of 13-16 seconds;</li> <li>The recording is taken on a windless day, and no extensive surf zone confuses the nearshore zone seaward of the plunge point;</li> <li>The sand stirred and suspended in the foreshore is visible both in the swash and in the water raised and curled as the wave breaks;</li> <li>The backrush from the previously broken wave has largely returned seawards when a fresh plunger engulfs the foreshore; this emphasises the cycling behaviour expected in a wave also as regards the sand motion;</li> <li>The breaking does not unfold as a single wave form seamlessly steepening, curling, and collapsing after a single point of instability has been touched. Instead, while advancing over the small plunge distance, the steep wave face spawns new crests of water that surge ahead and leave behind the previous crest. The trailing crests, nonetheless, impinge on the back of the leading wave face and break behind. The breaking of this 'single breaker' is, in fact, remarkably composite and nonlinear;</li> <li>Because of the considerable steepening, the plunging waves engulf as considerable a volume of air, which produces in turn a dramatic explosion of spray.</li> </ol> <p>This evidence on a natural beach can usefully be contrasted with the laboratory studies of <a href="https://doi.org/10.1002/2013JC009324" target="_blank" rel="noopener">Sumer et al (2013)</a> who compare the breaking of a train of plunging waves in a flume with and without a sand bed; and with the laboratory study of <a href="https://doi.org/10.1306/D4267B36-2B26-11D7-8648000102C1865D" target="_blank" rel="noopener">Hafsteinsson et al (2017)</a> who organise systematic observations of spilling, plunging and surging breakers in a narrow channel with a uniform bed slope.</p> <p>Finally, the following table comments on some twenty still frames. Selecting these frames entailed the dilemma of choosing times when a process either just initiates or is already developed enough to be recognisable; the pictures may thus regard both situations. The division into columns reflects fairly loosely a visual separation between either side of a fictional breaker line. I have strived to restrict the commentary to the phenomenological description of the sole free surface (hence avoiding inferences about the underlying flow patterns, however inviting, if self-evident). Please take note that the table only provides orientation and may be revised incrementally without notice later; see §4.2 on versions for substantive edits.</p> <h3>Table. Commentary of selected still frames</h3> <table> <tbody> <tr> <th>Frame</th> <th>Time (ms)</th> <th>Surf and swash on the foreshore</th> <th>Shoaling and breaking</th> </tr> </tbody> <tbody> <tr> <td>1</td> <td>0</td> <td>The swash of the previously broken wave covers the beach face. Water returns from the limit of wave uprush as a thin sheet of white water. A wide band of foamy water advances shorewards upon that; its front rolls up irregularly, with foamy filaments ejected upwards. Sand in suspension can be inferred from brown-shaded longshore streaks.</td> <td>A wide band of ripple-free water separates the foamy shoreward waters from the incoming shoaling waves. Short-crested wavelets populate the surface seawards of this middle band.</td> </tr> <tr> <td>28</td> <td> <p>1080</p> <p>[+1080]</p> </td> <td>The thin film on the upper foreshore has retreated significantly. Rolling water marks the edge of the thicker uprush. The ejection of filaments has terminated.</td> <td>The crest of a shoaling wave emerges over the image width; individual short-crested waves ride upon it. To the right, secondary fronts develop within a small cross-shore distance; subsequently, the foremost wave face hides their development from view.</td> </tr> <tr> <td>48</td> <td> <p>1880</p> <p>[+800]</p> </td> <td>The thin sheet of backrush water is exhausted. The foamy uprush starts to retreat.</td> <td>Extant ripples and wavelets still ride on the wave face as the latter steepens further.</td> </tr> <tr> <td>94</td> <td> <p>3720</p> <p>[+1840]</p> </td> <td>The water contour and surface are smooth on the landward edge. Hills and knobs of circulating white water populate the lower foreshore.</td> <td>The shoaling wave advances. Its face has steepened up considerably and cannot support extant ripples any longer; its surface becomes progressively smoother.</td> </tr> <tr> <td>107</td> <td> <p>4240</p> <p>[+520]</p> </td> <td>The white water retreats farther seawards. An edge with the deeper swash water steepens slightly. The disappearance of foam reveals the sand suspended in the swash.</td> <td>The front wave has travelled a short distance further shoreward and is very nearly vertical. Its crest is nearly horizontal and still sharply delineated; its contour starts to break up just afterwards.</td> </tr> <tr> <td>113</td> <td> <p>4480</p> <p>[+240]</p> </td> <td>Ditto.</td> <td> <p>The height of the crest varies alongshore; the part to the right attains its summit and its contour starts to break up.</p> </td> </tr> <tr> <td>126</td> <td> <p>5000</p> <p>[+520]</p> </td> <td>The landward edge of the swash steepens further and the face of this backwash shows a sand-rich mixture. The white water from the rear swash overtops this steep edge at places.</td> <td>The crest in the middle of the image attains its summit. Its break-up projects spray and translucent streaks of water upwards. Detached water hangs in the air because the crest drops faster than its fall speed. Rear waves catching up with the breaker, hence not on view, may also affect the break-up of the crest.</td> </tr> <tr> <td>129</td> <td> <p>5120</p> <p>[+120]</p> </td> <td>Ditto.</td> <td> <p>The fragmented fringe previously at the fore is left behind by a new face and crest that have surged forward. The water mass is translucent enough to show patches and streaks of suspended sand raising to the full height of the wave face. Streaks of bubbles dragged upward from the swash indicate that the wave steepening draws water from the foreshore.</p> </td> </tr> <tr> <td>141</td> <td> <p>5600</p> <p>[+480]</p> </td> <td>The swash front is a dense mixture of sand and water. Much of the white water on top of the rear swash has become rarefied and is dragged seawards by the raising breaker.</td> <td>The contour of the crest is wavy and has several local summits. The fragmentation into streaks, droplets and spray is intense; spray is ejected upwards, up to the level of the horizon. Conceivably, a wave front at the rear impinges the rear of the front wave.</td> </tr> <tr> <td>149</td> <td> <p>5920</p> <p>[+320]</p> </td> <td>Ditto.</td> <td>The wave base travels shorewards while the crest curls over. Dense clouds of sand entrained in suspension help identify the onset of a definite curling motion, accompanied by the marked lowering of the fringe height. A new crest fringe appears to surge forward from the parent wave, as seen previously.</td> </tr> <tr> <td>157</td> <td> <p>6240</p> <p>[+320]</p> </td> <td>The foreshore water is rich in suspended sand and poor in entrained air. The water surface is relatively flat.</td> <td>The crest at the front is curling forward. Visible in the background is also the curling of a trailing wave, confirming the composite nature of this breaker.</td> </tr> <tr> <td>159</td> <td> <p>6320</p> <p>[+80]</p> </td> <td>Ditto.</td> <td>The first foam of the curling water touches down upon the shallow swash water in a downward jet. It bounces on the beach face immediately afterwards. The same occurs in other positions with a time lag. Spray is still suspended in the air.</td> </tr> <tr> <td>168</td> <td> <p>6680</p> <p>[+360]</p> </td> <td>The backrush is, to an approximation, at its seaward visible limit.</td> <td>The plunging water has touched down over the image width. The water that is curling over is laden with sand. The splash generated by the rebound is projected shorewards and raises as high as the wave plunging at the same time. Farther seaward, a narrowly spaced train of short-crested waves is shoaling.</td> </tr> <tr> <td>175</td> <td> <p>6960</p> <p>[+280]</p> </td> <td>The swash is a thick layer of sand-rich mixture and has a flat surface.</td> <td>The splash generates pervasive spray and foam, high enough to hide the view of shoaling waves in the littoral. An inconspicuous hole in the wall of spray to the right of the image is a notable exception to that.</td> </tr> <tr> <td>186</td> <td> <p>7400</p> <p>[+440]</p> </td> <td>The spray of the breaker has engulfed all the sand suspended in the foreshore.</td> <td>White water (foam, bubbles and droplets) is propelled forwards and engulfs the sand-rich backrush on the foreshore, dominating the view.</td> </tr> <tr> <td>196</td> <td> <p>7800</p> <p>[+400]</p> </td> <td>The bulk of the splash water has collapsed. The surface is highly fragmented with plenty of ejections and rebounds, priming a fresh swash line to run up the beach face. The colour shades in the foreshore indicate abundant sand in suspension.</td> <td>At the rear of the previous plunge point, the trailing plunging wave rolls across the surf zone. Farther behind, to the left of the image, patches of white water erupt through the free surface. Overall, the height of waves and spray does not hinder the view of littoral waters: no shoaling waves are developing as yet.</td> </tr> <tr> <td>202</td> <td> <p>8040</p> <p>[+240]</p> </td> <td>The white water bounces on the shoreface forming patches of varying height. Foamy filaments break up into large drops. The breakers previously hidden from view are visible as a sequence of troughs. Mixtures of sand and foam are also visible to the left. The uprush advances above the saturated foreshore.</td> <td>Most spray has settled. The trailing waves stay low as they break and undergo eruptions of white water especially under their crests.</td> </tr> <tr> <td>250</td> <td> <p>9960</p> <p>[+1920]</p> </td> <td>White water runs up the foreshore vigorously. The ejection of filaments has died off almost completely and the water surface is crossed by foamy wavelets. The edge of the swash glides over the wet foreshore and leaps over at times. The seaward boundary of the white water is a sharp ridge moving slowly seawards.</td> <td>No shoaling wave emerges from the rear waters.</td> </tr> <tr> <td>291</td> <td> <p>11600</p> <p>[+1640]</p> </td> <td>In the upper foreshore a uniform milky film replaces the irregular patches of foam and sediment. In the middle of the surf, ephemeral fronts of white water sweep the foreshore, while rolling up and plunging.</td> <td>Ditto.</td> </tr> <tr> <td>336</td> <td> <p>13480</p> <p>[+1880]</p> </td> <td>The surf consists of the landward film of white water, sweeping the upper foreshore, and of the thicker seaward water. White water rolls up and breaks at the knobbly edge between these two regions.</td> <td>Qualitatively, this frame shows a remarkable similarity with frame 1, as for the extents of the run-up water and the ripple-free surface in the shoreface.</td> </tr> <tr> <td>390</td> <td> <p>15560</p> <p>[+2080]</p> </td> <td>The film of backrush water is exhausted almost completely. The edge of the swash is a gently rolling line. The surf area is fairly uniformly smooth.</td> <td>The water seaward of the surf is free of ripples for some distance. Farther seawards, ripples populate the surface; slightly steepened wave forms prelude to the crest of a fresh shoaling waves, like in frame 1.</td> </tr> </tbody> </table> <h1>2. Image manipulation</h1> <h2>2.1 Toolbox</h2> <p>Four open-source utilities have been used to produce this dataset: (1) `<a href="https://ffmpeg.org/ffprobe.html" target="_blank" rel="noopener">ffprobe version 4.2.7</a>` to determine the video properties; (2) `<a href="http://ffmpeg.org/about.html" target="_blank" rel="noopener">ffmpeg version 4.2.7</a>` to extract the stills from the video; (3,4) `convert` and `identify` from the <a href="https://imagemagick.org/" target="_blank" rel="noopener">ImageMagick tools version 6.9.10-23</a> to manipulate the stills and determine an image’s property respectively. The developers of these utilities claim that they run on a variety of operating system. Here all image processing has been carried out with, and proved to run successfully on, Linux.</p> <h2>2.2 Source video: specifications and characteristics</h2> <p>The source video is ogv format. The logical size of the image (improperly called resolution) is 1270x720 pixels; this corresponds to a pixel count of 914,400 (commercially presented as 0.9MP) and, approximately, to a 16:9 aspect ratio. The recording lasts (nominally) 15.6 seconds at a frame rate of 25 fps and contains 390 still frames spaced 0.04 s (40 ms) apart. The effective duration is 15.56 s.</p> <p>The operator holds the camera with a firm hand and the images are well lit and sharp. On close inspection, four glitches become apparent:</p> <ol> <li> <p>Lens distortion: the sea horizon is slightly curved upwards at the edges of the image, which indicates pincushion distortion (the image-to-object magnification rate increases away from the lens centre);</p> </li> <li> <p>Tilt: the camera view has a small anticlockwise roll angle with respect to the horizontal, whereby the sea horizon slopes slightly downwards to the right;</p> </li> <li> <p>Glare: the brightness of the images increases between approximatively 4 and 8 seconds of the recording; this overall glare is visible in the lightness of the sky and is arguably caused by the camera automatic diaphragm as it adjusts to the light reflected by the wave breaking;</p> </li> <li> <p>Motion: the horizon slightly shifts upwards at the tail of the video: this is most likely caused by the beach sand yielding under the operator’s weight as the uprush arrives and retreats on the foreshore.</p> </li> </ol> <p>The first two imperfections are remedied by manipulating the image, as described next.</p> <h2>2.3 Frame extraction with ffmpeg</h2> <p>The 390 still frames are extracted to as many stand-alone image files using the `ffmpeg` utility, which preserves the logical size of the frames. The image files are saved in tiff format. This format was chosen so that the tool `convert` does not bump into some memory restrictions encountered when manipulating png files as in next subsection. The output frames have a default pixel resolution of 72 dpi, which determines the expected physical size of the frame when printed. (The tool `convert` can also change this resolution by means of resampling, as described below.)</p> <p>The output file sizes vary slightly in the range 1307kB-1360 kB (base-10 file size) or 1276-1328 KiB (base-2 file size). The output colour format is standard RGB (sRGB), with a colour depth of 8 bit (256 shades available per colour channel). All 390 tiff images take 524MB (or 500MiB) of memory space. They are input for the `convert` utility as described next. They are not distributed with this deposit, but can be recreated with the script provided below as the need be.</p> <h2>2.4 Frame manipulation with convert</h2> <p>The sequence of `convert` operations to improve the final still frames is:</p> <ol> <li> <p>rotate the image to compensate for the tilt (target: the horizon is symmetric with respect to the vertical axis through the image centre);</p> </li> <li> <p>apply barrel distortion to the image to compensate the pincushion-type lens distortion (target: the horizon is a straight line);</p> </li> <li> <p>crop the image canvas (target: eliminate the vignetting due to the previous manipulations).</p> </li> </ol> <p>In theory, the correct order of operations should be 2-1-3. The bias of lens distortion is caused by the camera hardware and affects the entire field of view, regardless of how the camera is held. Determining the parameters of the compensating (barrel) distortion should thus have taken into account the distortion present in the entire field of view. This would have required evaluating the effect of lens distortion with a picture of a test card, such as a chessboard pattern. Here, however, the aim is mainly an aesthetic correction rather than extracting spatial information from the scene. Straightening up the horizon line is sufficient and can be done after having rotated the image, to the same visual effect obtained with the correct order.</p> <p>The logical size of all 390 manipulated images is 1240x670 pixels (aspect ratio 1.85). Their (default) resolution of 72 dpi (2.834 × 2.834 pixels/mm) means that their print size is 437.5 × 236.4 millimetres. The file sizes in png format vary in the range 750-1168 kB (732-1140 KiB). The complete set of images is 383 MB (365 MiB) large. These files are part of the deposit and their arrangement and naming are explained in Section 3.</p> <h2>2.5 Script</h2> <p>The script that performed the image extraction and manipulation is part of the deposit (named <em>script-image-extraction+manipulation.sh</em>). The script is written in GNU bash, version 5.0.17(1). Aside from the image-processing utilities already mentioned, the script also calls standard tools distributed in the GNU coreutils, version 8.30. GNU bash is a standard command-line interpreter in several Linux and MacOS distributions. Windows users could run it after installing the terminal emulator <a href="https://gitforwindows.org/" target="_blank" rel="noopener">Git for Windows</a>, for example. (Mac users, whose default shell interpreter is zsh, will experience troubles with # indicating comments in bash; please refer to this <a href="https://support.apple.com/en-au/HT208050" target="_blank" rel="noopener">Apple support article</a> on how to adjust that to bash.) The comments in the script, beside giving ‘sailing directions’, can serve as pseudocode if one wants to code the same workflow in another scripting language.</p> <p>Do not run this script blindly (some commands delete files). The script is divided into three sections. The first section defines the file paths, command parameters and other flags used in the remaining two sections, which deal with the image extraction and the image manipulation respectively. With this structure, the latter two sections need not to be edited for the script to do its job. The parameters and flags are set to the values used for this deposit and can be adjusted (the input and output paths should, for sure). Also, some commands only display information on the input and output documents before and after the processing. Among the possible usages, for example, one could change the default image resolution (dpi=72) to obtain images with a larger physical size by means of resampling, or change the output image format.</p> <p>Goes without saying: peruse the script and read the helps and manuals of the attending commands first.</p> <h1>3. Data arrangement</h1> <h2>3.1 Images</h2> <p>The 390 png images are arranged in <strong>15 zip archives</strong>, each containing one second worth of motion and hence 25 files (except for the 15 files of the last 0.56 seconds). The archive names indicate the <em>beginning</em> of the respective interval as lapsed time in milliseconds. The name format is <em>t[nnnnn]ms.zip</em>: for example, the archive <em>t05000ms.zip</em> contains the still frames between 5 and 5.960 seconds. The grand total size of the zip archives is 381 MB (363 MiB); the size of the individual archives varies in the range 16-29 MB (15-27 MiB).</p> <p>The name of the <strong>files inside the archives</strong> indicates the frame progressive number <em>and</em> the lapsed time in milliseconds in the format <em>f[nnn]-t[nnnnn]ms.png</em>. Note that the frame number starts from 1 and the lapsed time from 0.</p> <p>The deposit also includes, <strong>outside of the archives</strong>, the images at each second (the first file in each archive) in the way of covers that help pick up the time interval and zipped archive of interest. The covers name convention is the same as the archives (for example, <em>t05000ms.png</em> shows the first image contained in <em>t05000ms.zip</em>). You can preview these cover images in the section Files below.</p> <h2>3.2 Videos</h2> <p>The original, unprocessed video (<em>Pájara_-_Morro_Jable_-_Playa_del_Matorral_(0)_09.ogv</em>, 73 MB, 70 MiB) is also redistributed with this deposit and should be credited to Vincentz 2013 (see the section Licence for the conditions).</p> <p>Additionally, the processed images have been assembled in a video with the same duration as the original, and then in three more videos whose playback time is two-, four- and eightfold the physical time. These mp4 files have a name patterned as <em>breaker-video1-slow1x.mp4</em>. They are overlain by the frame number, the physical elapsed time, and the playback slow-down so as to help identify especially interesting frames. These slowed-down videos can be viewed in <a href="https://youtube.com/playlist?list=PLV5KQfKi7EFge-1gDEMyPGOlNCEQ9QDNM&feature=shared" target="_blank" rel="noopener">this YouTube playlist</a>. They are 8 (8), 11 (10), 13 (13) and 20 (19) MB (MiB) large respectively; their lengths are 22", 38", 1'9", and 2'11".</p> <p>Take note that making a video out of individual images implies dropping and duplicating frames. In particular, a slowed-down video is created by filling the longer playback time with frames interpolated from the baseline images. A slowed-down video helps gain appreciation of a rapid process, but cannot produce insight into events occurring at a faster rate than 40 ms anyhow. Therefore, the best representation of the ground truth must always be sought in the smallest recording units, that is, the individual 390 images taken at a rate of 25 fps.</p> <h1>4. This deposit</h1> <h2>4.1 How to cite this work</h2> <p>This commentary and dataset are indexed with a DOI <a href="https://doi.org/10.5281/zenodo.7601924">10.5281/zenodo.7601924</a>. The citation text is available in different styles in the box Share, to the upper right of this web page. (Goes without saying that grey literature should be acknowledged also in peer-reviewed literature.)</p> <h2>4.2 Versions</h2> <p>Major numbers indicate changes in the deposit content, minor numbers significant changes in the deposit Description (this web-based document you are reading now). A major version change implies Zenodo issuing a new DOI.</p> <p>The DOI <a href="https://doi.org/10.5281/zenodo.7601924">10.5281/zenodo.7601924</a> always points to the latest version. The table below displays the history of versions. This deposit has been created on 11 Feb 2023. I adjust the date of publication of the deposit to the latest version, so that the automatic citations provided by Zenodo report consistent date/version information.</p> <h3>List of versions</h3> <table> <tbody> <tr> <th>v2.5</th> <td>24/01/2025</td> <td>Revise licensing terms</td> <td><a href="../record/8070591">https://zenodo.org/record/8070591</a></td> </tr> <tr> <th>v2.4</th> <td>09/03/2024</td> <td>Revise §1</td> <td><a href="../record/8070591">https://zenodo.org/record/8070591</a></td> </tr> <tr> <th>v2.3</th> <td>18/09/2023</td> <td>Add link to video playlist</td> <td><a href="../record/8070591">https://zenodo.org/record/8070591</a></td> </tr> <tr> <th>v2.2</th> <td>22/07/2023</td> <td>Complete table in §1.3</td> <td><a href="../record/8070591">https://zenodo.org/record/8070591</a></td> </tr> <tr> <th>v1.2</th> <td>22/06/2023</td> <td>Strip description after v2.1</td> <td><a href="../record/7601925">https://zenodo.org/record/7601925</a></td> </tr> <tr> <th>v2.1</th> <td>22/06/2023</td> <td>Add videos of dataset</td> <td><a href="../record/8070591">https://zenodo.org/record/8070591</a></td> </tr> <tr> <th>v1.1</th> <td>21/06/2023</td> <td>Add commentary to §1</td> <td><a href="../record/7601925">https://zenodo.org/record/7601925</a></td> </tr> <tr> <th>v1.0</th> <td>11/02/2023</td> <td>Publish images</td> <td><a href="../record/7601925">https://zenodo.org/record/7601925</a></td> </tr> </tbody> </table> <h2>4.3 Next</h2> <p>The current wish-list contains: a) linking the script to a GitHub repository if its complexity grows; b) comment the state of the free surface using the terminology of Brocchini and Peregrine (2001), even though their study was prompted by spilling breakers; c) include other videos; d) publish videos in ogv format.</p>
Comparative Analysis of Droplet- vs. Microwell-based Whole Transcriptome Single-Cell Sequencing Technologies in Complex Human Tissues
<p>In the past decade, high-dimensional single-cell omics tools have enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, recent investigations suggest that each technique has its unique strengths but also technology-inherent limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromium <em>vs.</em> microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy.</p> <p>Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of detectable cell populations differed. This could in part be ascribed to differences in the performance to recover cells with low-mRNA content. Hence, immune cells such as neutrophils are underrepresented in data generated with the widely used droplet-based scRNA-seq protocol, highlighting the importance of considering platform limitations in low mRNA content cell recovery. In contrast, droplet-based scRNA-seq demonstrated superiority in terms of recovering cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation, affecting the composition of identified tissue profiles and the exploratory value of the generated datasets. Overall, our study emphasizes the importance of carefully selecting the appropriate scRNA-seq platform to improve cell type representation and obtain a more comprehensive and accurate understanding of the TME.</p>
ValEqt: A high-resolution Earthquake and Repeating earthquakes catalog of the 2017 Valparaiso sequence
<p><strong>The ValEqt earthquake catalog</strong></p> <p>Description:</p> <p>Catalog of earthquakes detected near the 2017 Mw=6.9 Valparaiso (Chile) earthquake from 01/01/2016 to 01/01/2021. We also include a catalog of ValEqt's repeating earthquakes.</p> <p>Methods used to build this dataset are extensively described in this paper : <em>Upcomming paper Doi</em></p> <p>Files:</p> <ol> <li><em>ValEqt.txt </em>: Earthquake catalog</li> <li><em>Repeater.txt</em> : Repeating earthquake catalog</li> </ol> <p> </p>
Supplementary data for: DNA sequences are as useful as protein sequences for inferring deep phylogenies
<p>Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences, based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies.</p>
Genome sequencing of 2,000 canids advances the understanding of demography, genome function and architecture
<p><strong>Background: </strong>The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20x data from 1,987 individuals, including 1,611 dogs (321 breeds), 309 village dogs, 63 wolves and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility and genome architecture and function.</p> <p><strong>Results: </strong>We report the analysis of >48M single nucleotide, indel, and structural variants spanning the autosomes, X chromosome and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.</p> <p><strong>Conclusions:</strong> We have developed a dense dataset of 1,987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available</p>
Reproduction package for the paper "Massive pre-main-sequence stars in M17: Firtst and second overtone CO bandhead emission and the thermal infrared"
<p>This is a basic reproduction package for the paper "Massive pre-main-sequence stars in M17: First and second overtone CO bandhead emission and the thermal infrared" by J. Poorta et al. 2023. It aims to provide the most important data products and software to check and reproduce the main results of the paper.</p>
FIG. 2 in Structural and functional genes, and highly repetitive sequences commonly used in the phylogeny and species concept of the phylum Cyanobacteria
FIG. 2. — Phylogeny of common or less studied genetic markers. According to the literature review,less common studied genetic marker has been highlighted.
FIG. 1. — A in Structural and functional genes, and highly repetitive sequences commonly used in the phylogeny and species concept of the phylum Cyanobacteria
FIG. 1. — A summary of structural and functional genes, and highly repetitive sequences commonly used in the phylogeny of cyanobacteria.
Prospects for a sequence-based taxonomy of influenza A virus subtypes
<p>This dataset comprises the multiple sequence alignments (*.fasta) and maximum likelihood phylogenies (Newick tree strings, *.nwk) for all available protein sequences corresponding to the eight genome segments of influenza A virus from the NCBI Genbank database. </p> <p>Each sequence is labelled with the Genbank accession number (e.g., "CY103884"), WHO strain identifier ("A/little yellow-shouldered bat/Guatemala/164/2009"), subtype label ("H17N10"), host species ("Sturnira lilium; gender M"), sampling location ("Guatemala: El Jobo"), and sample collection date ("May-2009"). These fields are separated by underscore characters.</p> <p>These data are provided under a Creative Commons license in support of a manuscript in progress, "Prospects for a sequence-based taxonomy of influenza A virus subtypes".</p>
Genomic characterization and gene bank curation of Aegilops using genotyping-by-sequencing
<p>In this study, genotyping-by-sequencing (GBS) was performed on 1041 <em>Aegilops</em> accessions, representing 23 different species. These accessions have been maintained by the Wheat Genetics and Resource Center (WGRC) at Kansas State University. The GBS FASTQ files have been uploaded to the NCBI SRA public repository under the BioProject accession number # PRJNA985892. We have provided other files related to data analysis, such as the barcode key file, SNP matrices, and taxonomic information of the accessions in this Dryad repository, which can be accessed through the provided link. The aim of the study was to explore the genetic and genomic characteristics of wild wheat relatives, <em>Aegilops,</em> using a larger number of SNP markers. Here, we also curated the WGRC gene bank <em>Aegilops</em> collection via the identification of misclassified accessions and genetically identical redundant accessions. Further, we explored the genomic relationship between wheat and the different <em>Aegilops</em> species. </p>
Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing
<p>Supplementary data that are needed to rerun the reproducible notebooks from the first steps using Alevin output and configuration files.</p> <p>Intermediate R data object that can be used to rerun the reproducible notebooks after the filtering steps.</p> <p>Validation data for inferring the sample index hopping rate. The <em>hiseq4000_joined_datatable_plexed_nonplexed.zip file contains read counts for four samples (two non-multiplexed and two multiplexed) joined by a cell-barcode, UMI, and gene-ID (CUG) key combination. The hiseq4000_inner_joined_with_labels.zip file contains only those CUGs that are observed in both the non-multiplexed and multiplexed samples.</em><em> </em></p>
The daft genome sequences for the isolated viruses.
<p>The daft genome sequences for the viruses isolated from Lake Biwa, Japan. The genomes were sequenced by MinION and assembled by Flye, Miniasm, and Raven, followed by short-read polish by using Pilon. </p>
ScienceDex guides
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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.