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38,569 results for “c”
Comparing vertical accretion, organic carbon (C) sequestration, and nitrogen burial between a natural, never diked tidal salt marsh and a hydrologically restored tidal salt marsh on Sapelo Island, Georgia.
Restoration of tidal marshes throughout the 20th century have attempted to bring back important functions of natural tidal systems. In this study, vertical accretion, organic carbon (C) sequestration, and nitrogen burial were compared between a natural, never diked tidal salt marsh and a hydrologically restored tidal salt marsh on Sapelo Island, Georgia to examine the impacts of restoration years later. On Sapelo Island there are two marshes near the University of Georgia Marine Institute, one of which is a natural marsh, and one of which is a restored marsh. The restored marsh had been diked in 1948, and the dike was breached, allowing for the marsh to be restored, in 1956. Soil cores were collected from both marshes, and the sediments were analysed for Nitrogen and Carbon concentrations and bulk density. This analysis was used to determine accretion rates for the two marshes as well as changes in the restored marsh since the dike was breached. Nitrogen burial, carbon sequestration, and soil accretion in the restored marsh as compared to the natural marsh were the focus of this study.
Dataset of "Thermal Stability of Valuable Metals in Lithium-Ion Battery Cathode Materials: Temperature Range 100-400 °C"
<p>Lithium is crucial in lithium-ion batteries (LIBs), serving as a main component of the electrolyte and cathode. Elements such as cobalt, nickel, and manganese are also vital for high performance, energy density, and stability. This study aimed to examine the behaviour of end- of-life cathode material (LiNi0.6Mn0.2Co0.2O2) and its valuable metals after exposure to temperatures between 100 and 400 °C, comparing it with untreated material. The lithium content cannot be reliably determined by conventional analytical methods, so inductively coupled plasma optical emission spectroscopy (ICP-OES) was chosen for this purpose. For ICP-OES measurements, samples were dissolved in different solvents for a specified time, and the concentrations of lithium, nickel, manganese, and cobalt were measured. From the measured values, their theoretical yields were calculated. Due to the annealing at given temperatures and subsequent dissolution, this step can be considered as the first stage of the pyrometallurgical- hydrometallurgical process used in battery recycling. The study was complemented by further analyses to monitor the effect of annealing temperatures on the properties of the material. Based on the results, it was found that the highest theoretical yield in this temperature range was for material annealed at 400 °C and dissolved in 20% nitric acid for 4 hours.</p>
C Concentrations and Characterization Data from DOM Incubation Assay Experiments
This dataset includes (1) original data from a dissolved organic carbon (DOC) incubation experiment and (2) a data synthesis of the DOC incubation experiment literature. Study component (1) was a factorial lab experiment crossing varying dissolved organic matter (DOM) sources (Suwannee River Fulvic Acid, Elliott soil leachate, Chlorella leachate) with varying microbial communities. The objective of this study component was to test the interacting effects of microbial community composition and DOM characteristics on carbon (C) biodegradation. We used a Micro-Oxymax Respirometer (Columbus Instruments, Columbus, Ohio) to measure carbon dioxide and oxygen accumulation at two hour intervals for a period of two weeks, and quantified the initial and final concentrations of dissolved organic carbon and total dissolved nitrogen of each experimental unit. To verify that the three DOM source solutions had differing chemical compositions and potential bioreactivity, we optically characterized each DOM source using mass spectra analysis and excitation-emission matrices (EEMs). Study component (2) is a synthesis of DOC concentrations from the C degradation experiment literature. The criteria for including a study in this synthesis was that (a) incubation DOM was sourced from a river, lake, marine, estuary, or marsh, and (b) that C concentrations were measured at least twice throughout the incubation in addition to an initial measurement. For each study, we extracted initial DOC values, elapsed incubation time, and reported DOC concentrations during the incubation period for each experimental treatment. This data package is completed.
Long term response of arctic tussock tundra to thermal erosion features: A modeling analysis. Tussock tundra regrowth after a thermal erosion event: Simulation C - increased Phase I and Phase II soil organic matter
The Multiple Element Limitation (MEL) model is used to simulate the recovery of Alaskan arctic tussock tundra to thermal erosion features (TEFs) caused by permafrost thaw and mass wasting. TEFs could be significant to regional carbon (C) and nutrient budgets because permafrost soils contain large stocks of soil organic matter (SOM) and TEFs are expected to become more frequent as climate warms. These simulations deal only with recovery following TEF stabilization and do not address initial losses of C and nutrients during TEF formation. To capture the variability among and within TEFs, we simulate a range of post-stabilization conditions by varying the initial size of SOM pools and nutrient supply rates. This file contains the results for 100 years of tussock tundra recovery after a thermal erosion event. This simulation is of TEF recovery with increased Phase I and Phase II soil organic matter compared to the base simulation. Data is presented for day 250 of each year.
Cobalt-Mediated Photochemical C−H Arylation of Pyrroles
<p>Optimized geometries in xyz-format, supplement to the journal article published in <em>Angew. Chem. Int. Ed. </em><strong>2024</strong>, e202405780 (<a href="https://doi.org/10.1002/anie.202405780">https://doi.org/10.1002/anie.202405780</a>).</p>
Supplementary dataset to publication: Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes.
<p>This is the modified supplemented material to the publication “Complete genome sequence of ovine Mycobacterium avium subsp. paratuberculosis strain JIII-386 (MAP-S/type III) and its comparison to MAP-S/type I, MAP-C, and M. avium complex genomes”.</p> <p>The complete circular genome of Mycobacterium avium subsp. paratuberculosis (MAP) strain JIII-386 from Germany, closed by Nanopore technology in this study, was presented and compared with the draft genome of JIII-386, previously published in [doi:10.1093/gbe/ew154], the closed genome of the MAP-S/type I strain Telford, the MAP-S/type III draft genome of strain S397, twelve closed MAP-C (type II) strains and eight closed Mycobacterium avium (M. a.) strains of subsp. hominissuis (MAH) and subsp. avium (MAA). Structural comparisons clearly revealed the mosaic nature of MAP genomes, the differences between MAP subtypes I, II and III, and the higher diversity of MAP-S compared to MAP-C genomes. </p> <p>The material provides a wealth of detailed results from these analyses and comparisons. These include a list of identified ncRNA and Riboswitches, as well as additional genes in finished JIII-386, the gene content of identified prophage regions, copy number of identified transposable elements and a list of selected virulence-associated genes in the different MAP-type (I - III) strains. The genomic islands identified and included genes along with their predicted functions were presented for six MAP genomes (belonging to MAP-S/type I and III, and MAP-C), one MAH genome and one MAA genome. One table shows the corresponding genomic islands in the genomes of JIII-386, Telford and three MAP-C genomes. Furthermore, homologous genes of known MAP-S specific Large Sequence Polymorphisms regions (LSP<sup>S</sup> = LSP-S) were recorded in different MAP-S type strains, one MAH and one MAA strain, as well as genes of deletions #1 (LSP<sup>A</sup>-20), #2, and s-delta-1, previously described as MAP-S-specific deletions, their presence or absence in 3 MAP-S, 12 MAP-C, 4 MAH, and 4 MAA strains were listed. Different presence or absence of genes, but also identified frameshifts or disruptions of various virulence-associated genes could lead to the different MAP-type specific phenotypic characteristics. Comprehensive core and pan genome analyses (results listed in six tables) revealed unique genes and genes likely to have been acquired by horizontal gene transfer in different MAP types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M. a. strains.</p> <p> </p>
Dataset of "Impact of Carbon Corrosion and Denitrogenation on the Deactivation of Fe-N-C Catalysts in Alkaline Media"
<p>In this work, we use a gas diffusion electrode half-cell coupled with inductively coupled plasma mass spectrometry (GDE-ICP-MS) to quantify the Fe dissolution rates in the potential range between 0.93 and 1.5 VRHE. It is shown that Fe dissolution accelerates with increased anodic potential and temperature while it is independent on the presence/absence of O2. The onset potential of Fe dissolution at room temperature agrees with the reported onset potentials of carbon corrosion and denitrogenation, C and N being oxidized to gaseous COx and NOx species, respectively. This correlation supports that the electrochemical oxidation of the N-C matrix triggers the observed catalyst demetallation in these conditions. Using a set of ex situ physicochemical characterization techniques, including spectroscopy and microscopy, the various degrees of degradation under three sets of experimental conditions of interest (O2-RT, O2-HT, and Ar-HT, where RT = 22℃ and HT = 62℃) are rationalized. Combining the GDE-ICP-MS technique and post-mortem analyses, this work provides novel insights into the degradation pathways of various Fe, N, and C species during start-stop events, which may inspire the next generation of durable Fe-N-C catalysts for anion exchange membrane fuel cells.</p>
Dataset of "Asparagine-Modified Magnetic Graphene Oxide: An Efficient and Green Nanocatalyst for Synthesis of 5-oxodihydropyrano[3,2-c]chromenes and dihydropyrano[2,3- c]pyrazole derivatives and the Density functional theory calculation".
<p>The primary focus of this study involved the fabrication of a novel nanocatalyst Fe3O4-supported asparagine functionalized graphene oxide (Fe3O4@GO-N-(Asparagine)). The catalyst was synthesized through a four-step procedure.</p>
Daily water temperature (C) in the Yolo Bypass and Sacramento River, 1998-2019
This data is an integration of raw logger data as well as relevant California Data Exchange Center (CDEC) data (Pien et al. 2020, hourly) and water quality data collected during the Yolo Bypass Fish Monitoring Program’s (YBFMP) fish collection (Pien and Kwan 2022) to produce a daily water temperature dataset for the Yolo Bypass and Sacramento River at Sherwood Harbor and Rio Vista Bridge. The raw YBFMP’s water temperature data was collected by loggers attached to the rotary screw trap (STTD) and Sherwood Harbor (SHR). Logger data ranged from daily means (1998) to a fifteen-minute collection interval (2013-2017 for the Yolo Bypass, 2009-2019 for Sherwood Harbor). A daily mean, maximum, minimum, standard deviation and coefficient of variation in water temperature was produced as well as columns for sample size (n, number of measurements per day), method (data collection or estimation), category, length (number of consecutive missing dates) and site. Daily water temperature data for the full extent of the YBFMP’s fish collection is valuable for a variety of purposes. For example, variation in water temperature during inundation and comparisons between temperatures in the Sacramento River and Yolo Bypass have been used as metrics of habitat complexity and linked to life history diversity in salmon (Goertler et al. 2017).
Pond Cypress C-111 Basin, Everglades (FCE), South Florida Dendroisotope Data from 1970 to 2000
δ13C values were determined from cypress tree rings from two different study areas in South Florida. One site is located in the Southeastern Everglades Marsh, where pond cypress (Taxodium ascendens) was sampled from tree islands (annual tree rings from 1970 to 2000). Bald cypress (Taxodium distichum) trees were sampled at the other site, located along the Loxahatchee River in a coastal wetland (decadal tree rings from 1830 to 1990). The isotopic time series from both sites display different, location-specific information. The pond cypress isotopic time series has a positive correlation with the total amount of annual precipitation, while the bald cypress data from the Loxahatchee River study area had two different records dependent on the level of saltwater stress. In general, for terrestrial trees growing in a temperate environment, water stress causes an increase in water-use efficiency (WUE) resulting in a relative 13C enrichment. Yet, trees growing in wetland settings in some cases do not respond in the same manner. We propose a conceptual model based on changes in carbon assimilation and isotopic fractionation as controlled by differences in stomatal resistance (water stress) and mesophyll resistance (biochemical and nutrient related) to explain the isotopic records from both sites. With further work and a longer time series, our approach may be tested, and used to reconstruct change in hydroperiods further back in time, and potentially provide a baseline for wetland restoration.
Evaporation Estimates for Long Key C-MAN Weather Station, Florida Bay (FCE) from July 1998 to May 2004
This file contains data from the National Data Buoy Office Coastal-Meteorological Automated Network (C-MAN) weather station near Long Key, in Florida Bay (LONF1, 24deg 50min 36sec N, 80deg 51min 42sec W). The time period is 1600 EST February 6, 2004 through 0700 EST May 28, 2004. The record is a combination of NDBO data (wind speed, air pressure, air temperature water temperature) and Harbor Branch data (relative humidity) needed to calculate evaporative water loss. The file is one of several from this location. Together, they can be used to estimate of hourly, daily, monthly, seasonal and annual evaporation rates. Calculations include hourly water loss and cumulative water loss. Times are Eastern Standard.
Co-dominant removal and N and C fertilization experiment for moist meadow tundra, 2002 - 2018.
In 2002 seven experimental sites were set up in areas of moist meadow alpine tundra on Niwot Ridge. At each site, ten 1 m^2 plots were established where there was roughly even cover by two dominant plant species, Geum rossii (forb) and Deschampsia cespitosa (grass). In a factorial design, plots were assigned treatments of 1) removal of G. rossii, D. cespitosa, or control (no plant removal), and 2) nutrient addition of nitrogen (N), carbon (C), or control (no addition). A tenth plot was assigned a treatment of random biomass removal and no nutrient addition. Plots were visited annually to implement removal and fertilization treatments, and to measure plant species composition. Plant productivity was measured every other year and nematode communities once via 18S rRNA metabarcoding, together with soils. Carbon addition plots were dropped from the experiment in 2016.
ADS-C Air Traffic Data Collected by the OpenSky Network
<p>ADS-C data collected by the OpenSky Network since 7th July 2023. </p> <p>Data underlying (Version 1.1)</p> <h1>A First Look at Exploiting the Automatic Dependent Surveillance-Contract Protocol for Open Aviation Research</h1> <p>https://journals.open.tudelft.nl/joas/article/view/7229</p>
Study of Calabrian Sounding Objects. Interview and Field Notes - C. Macchione
<p>This dataset contains the ethnomusicological data concerning the study of traditional sounding objects in Calabria generated for the EU-funded research LoMus - Local Sound for a New Musicality. </p><p> </p><p>LoMus - Local Sound for a New Musicality. Enhancing Musical Participation through a Local Sonic Practice is a research project funded under the Marie Skłodowska Curie Action. LoMus investigates ways of expanding musical participation through the use of sounding objects and contemporary music techniques.</p>
Multi-faceted analyses of Poland's Bronze and Early Iron Age hoards: Fig.5. Pottery (A, C), animal bones (B), a human skull (C, D), and a flint tool (D) excavated from underneath the stone layer in Kaliszany (archaeological site no. 3)
<p>The set contains a figure, with with photographs that show examples of finds discovered during excavations at archaeological site 3 in Kaliszany, Wągrowiec commune, Poland. It is a stone and earth structure in which a hoard of metal objects dating to the Late Bronze Age was discovered in 1943. The photo is from the 2022 survey, when the south-western part of the structure was explored. <br><br>The paper and data were prepared as part of a project funded by the National Science Centre, Poland: <em>A Biography of Late Bronze and Early Iron Ages Hoards. A Multi-Faceted Analysis of Metal Objects Related to Monumental Constructions in Poland</em> (UMO-2021/41/B/HS3/00038)</p>
Dataset of "Liquid-Jet Photoemission Spectroscopy as a Structural Tool: Site-Specific Acid-Base Chemistry of Vitamin C"
<p>Liquid-jet photoemission spectroscopy (LJ-PES) directly probes the electronic structure of solutes<br>and solvents. It also emerges as a novel tool to explore chemical structure in aqueous solutions, yet<br>the scope of the approach has to be examined. Here, we present a pH-dependent liquid-jet photoelectron<br>spectroscopic investigation of ascorbic acid (vitamin C). We combine core-level photoelectron<br>spectroscopy and ab initio calculations, allowing us to site-specifically explore the acid-base chemistry<br>of the biomolecule. For the first time, we demonstrate the capability of the method to simultaneously<br>assign two deprotonation sites within the molecule. We show that a large change in chemical shift<br>appears even for atoms distant several bonds from the chemically modified group. Furthermore, we<br>present a highly efficient and accurate computational protocol based on a single structure using the<br>maximum overlap method for modeling core-level photoelectron spectra in aqueous environments.<br>This work poses a broader question: To what extent can LJ-PES complement established structural<br>techniques such as nuclear magnetic resonance? Answering this question is highly relevant in view<br>of the large number of incorrect molecular structures published.</p>
BGC-Argo Satellite matchup to compute variability in the Chl:C ratio of phytoplankton.
<p>This dataset provides matchups between BGC-Argo and MODIS satellites (both atmospheric and ocean color products). This dataset allows users to compare the variability of the Chlorophyll (Chl) to Phytoplankton Carbon ratio from BGC-Argo floats depending on the light in the mixed layer and link to information obtained from satellites about cloud coverage. </p> <p>Quality control previously performed on this dataset and matchup criteria are described in the associated publication.</p> <p>Here are some of the column headers detailed for clarity:</p> <p>Columns 1-25 represent data from the BGC-Argo floats:</p> <ul> <li>ID: Float WMO ID number</li> <li>dt: Datetime in datenum format.</li> <li>biomes: Biomes according to Fay & McKinley, 2014 (with West Mediterranean biome 18 and East Mediterranean biome 19)</li> <li>zenith: Sun zenith angle at time of surfacing.</li> <li>kd_490_Xing: Downwelling diffuse attenuation coefficient at 490nm from Xing et al.,2021 method. </li> <li>kd_PAR_Xing: Downwelling diffuse attenuation coefficient of PAR from Xing et al.,2021 method. </li> <li>chla: Median chlorophyll from fluorescence in the mixed layer (corrected for Non-Photochemical Quenching following Xing et al., 2012)</li> <li>F_indiv: Calibration factor for chla (chlorophyll from fluorescence) according to the method described in Xing et al., 2011. </li> <li>F_median: Median Correction factor (F) for all the floats in a biome</li> <li>F_median_season: Median Correction factor (F) for all the floats in a biome in a given season</li> <li>Chl_cor: Chla from floats corrected using the F_median factor according to Xing et al., 2011. </li> <li>PAR_0_Argo: PAR(0-) right below the surface also from Xing et al., 2021.</li> <li>Z_iso : Depth of the 0.415 mol/quanta/m-2/d-1 isolume. </li> <li>Zeu: Euphotic depth, 1% of surface light.</li> <li>Eg_Argo: Median light level in the mixed layer during a float's profile, bounded by the surface and the MLD (in mol quanta m^-2 h^-1).</li> <li>MLD: Mixed layer depth, determined using the 0.03 density criteria from de Boyer Montégut, et al.,2004.</li> <li>bbp_XXX: Backscattering at a specific wavelength</li> <li>Cphyto: Median Phytoplankton Carbon in the mixed layer computed from Bbp following Graff et al., 2015.</li> <li>Cphyto_B: Median Phytoplankton Carbon in the mixed layer computed from Bbp following Behrenfeld et al., 2005.</li> <li>Cphyto_M: Median Phytoplankton Carbon in the mixed layer computed from Bbp following Martinez-Vincente et al., 2013.</li> <li>ratio_cor: Chl_cor /Cphyto.</li> </ul> <p>Columns 26-45 have products from matchups with ocean-color MODIS files:</p> <ul> <li>sat_dt: Datetime of satellite overpass in datenum format. </li> <li>chlor_a: Satellite chl obtained from NASA's OBPG hybrid algorithm.</li> <li>sat_IPAR: Instantaneous PAR at time of overpass.</li> <li>sat_PAR: MODIS Daily PAR product above the surface.</li> <li>sat_Daily_PARminus: MODIS Daily PAR product propagated right below the surface (0-)</li> <li>sat_Daily_Eg: Daily median light in the mixed layer computed as sat_DailyPAR_minus * exp(-Kd_PAR*MLD/2) ( in mol quanta m^-2 d^-1).</li> </ul> <p>Columns 46-49 have products from matchups with atmospheric MODIS files: </p> <ul> <li>a_lat, a_lon, a_dt: Same as above but for the atmospheric file</li> <li>Confident Cloudy: Number of pixels (Out of 25) with the Confident Cloudy flag. </li> </ul> <p> </p>
Coherence and indistinguishability of highly pure single photons from non-resonantly and resonantly excited telecom C-band quantum dots
<p>ABSTRACT</p> <p>The role of resonant pumping schemes in improving the photon coherence is investigated on InAs/InGaAs/GaAs quantum dots (QDs) emitting in the telecom C-band. The linewidths of transitions of multiple exemplary quantum dots are determined under above-band pumping and resonance fluorescence (RF) via Fourier-transform spectroscopy and resonance scans, respectively. The average linewidth is reduced from (9.74 ± 3.3) GHz in the above-band excitation to (3.50 ± 0.39) GHz under RF underlining its superior coherence properties. Furthermore, the feasibility of coherent state preparation with a fidelity of (49.2 ± 5.8) % is demonstrated, constituting a first step toward on-demand generation of coherent, single, telecom C-band photons directly emitted by QDs. Finally, two-photon excitation of the biexciton is investigated as a resonant pumping scheme. A deconvoluted single-photon purity value of 𝑔(2)HBT(0)=0.072 ± 0.104 and a postselected degree of indistinguishability of 𝑉HOM=0.894 ± 0.109 are determined for the biexciton transition. This represents another step in demonstrating the necessary quantum optical properties for prospective applications.</p>
Supplemental data for characterization of alpha and beta interactions using the HeXe setup [Eur. Phys. J. C 82, 361]
<p>Repository with supplemental data to:<br> <strong>Characterization of alpha and beta interactions in liquid xenon</strong>. Jörg, F., Cichon, D., Eurin, G. <em>et al. Eur. Phys. J. C</em> <strong>82, </strong>361 (2022) <a href="https://doi.org/10.1140/epjc/s10052-022-10259-3">10.1140/epjc/s10052-022-10259-3</a><br> A pre-print of the article is available <em>on arXiv: </em><a href="http://arxiv.org/abs/2109.13735">2109.13735</a></p> <p><strong>Note: </strong>When re-using the data, please make sure to cite the article (and not only the dataset)</p> <p><br> The files contain the measured data points (as well as their statistical and systematic uncertainties) as shown in the publication.<br> All datasets are stored in the .csv format.</p> <ul> <li><strong>20210924_yields_hexe_kr83m.csv</strong><br> This file contains the normalized light and charge yields as a function of the applied field from the measurement with the <sup>83m</sup>Kr source. The data is shown in Figure 16 (dots) of the publication. Furthermore the file contains the LY ratio between the two Isomeric transitions of the <sup>83m</sup>Kr source, shown in Figure 17 of the article.</li> <li><strong>20210924_yields_hexe_rn222.csv</strong><br> This file contains the normalized light and charge yields as a function of the applied field from the measurement with the <sup>222</sup>Rn source. The data is shown in Figure 18 (blue-ish points) of the publication</li> <li><strong>20210924_drift_velocity_hexe_rn222.csv</strong><br> This file contains the measured electron drift velocity in liquid xenon at a temperature of 174.4 K in dependence of the field. The data was acquired using the <sup>222</sup>Rn source. Drift velocity is given in units of mm/µs and the datapoints are shown in Figure 20 (black dots) of the publication </li> <li><strong>20210924_drift_velocity_hexe_kr83m.csv</strong><br> This file contains the measured electron drift velocity in liquid xenon at a temperature of 174.4 K in dependence of the field. The data was acquired using the <sup>83m</sup>Kr source. Drift velocity is given in units of mm/µs and are not displayed in the publications due to visibility reasons.</li> </ul> <p><strong>Minimum working example to plot the drift velocity using the <sup>83m</sup>Kr data:</strong></p> <pre><code class="language-python"> 1 import numpy as np 2 import matplotlib.pyplot as plt 3 4 # load the data set 5 data = np.loadtxt("20220427_drift_velocity_hexe_kr83m.csv", delimiter=",") 6 7 # Plot the systematic uncertainty on the drift field 8 plt.errorbar(data[:,0], data[:,2], xerr=data[:,1], fmt="o", capsize=2, ecolor="darkgray", 9 alpha=0.7, elinewidth=3, color="black") 10 11 # Plot the actual data points 12 plt.errorbar(data[:,0], data[:,2], yerr=data[:,3], fmt="o", color="black") 13 14 # Label the axis and define the range 15 plt.ylabel("Drift Velocity [mm/µs]") 16 plt.xlabel("Drift Field [kV/cm]") 17 plt.xscale("log") 18 plt.xlim(0.006, 2) 19 plt.ylim(0, 2.4) 20 plt.show() </code></pre> <p> </p>
Test datasets for Hi-C scaffolding
<p>We provided two datasets for testing Hi-C scaffolding tools. For the CHM13 test dataset, we randomly chunked the first 10Mb of chr1, chr2 and chr3 of the T2T-CHM13v1.1 human genome assembly (Nurk et al. 2022) into 57 contigs. The Hi-C data downloaded from the telomere-to-telomere consortium GitHub repository (https://github.com/marbl/CHM13) were mapped to the reference genome and the reads mapped to these regions were extracted to generate Hi-C alignment files. For the LYZE01 test dataset, the Saccharomyces cerevisiae strain W303 genome assembly (Matheson et al. 2017) was split at positions with gaps (‘N’) to get the original contigs. An independent Hi-C data library was downloaded from the NCBI repository (GEO Accession GSM2417297) and downsampled to approximately 20X. The downsampled Hi-C data were mapped to the contigs to generate Hi-C alignment files.</p> <p>We provided five files for each test dataset: the contig file in FASTA format, the FASTA index file generated with SAMtools faidx command, and the Hi-C alignment file in BAM format sorted by coordinate, in BAM format sorted by query names (with the identifier 'qn' in the file name), and in BED format.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.