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Number of seasonal cycles of vegetation at global scale AVHRR
<p>Using the AVHRR product provided by NOAA, the NDVI time series has been calculated, a periodogram has been made to study different factors that affect the periodicity of the vegetative cycles. In this case, the number of seasonal cycles of vegetation.</p> <p>Value 1: one cycle</p> <p>Value 2: two cycles</p> <p>Value 3: three cycles</p>
Low Reynolds number response of a symmetric airfoil to viscous vortical gusts
<p>The response of a NACA0012 airfoil impacted by viscous vortical gusts at low Reynolds numbers is investigated performing Direct Numerical Simulations of the two-dimensional incompressible flow. This database contains the time history of the aerodynamic force coefficients of the airfoil during the interaction with the vortical gust. The airfoil, set at a fixed angle of attack alpha, is impacted by Taylor/Lamb-Oseen vortical gust, which are characterized by a diameter <em>D</em>, a intensity <em>v<sub>0m</sub></em>, and a vertical separation <em>h</em>. Direct Numerical Simulations are run for a range of values for the angle of attack, the size and intensity of the vortical gust, and the vertical separations. All simulations are run at a fixed Reynolds number Re=1000, based on the airfoil chord <em>c</em> and the free-stream velocity <em>U<sub>∞</sub></em>.</p> <p>More details on the database and the corresponding simulations can be found in Martínez-Muriel & Flores (2020), Analysis of vortical gust impact on airfoils at low Reynolds number, J. Fluids and Struct, 99. </p> <p><strong>Contents</strong><br> The database consist on a single ASCII file for each case. After a short, self-explanatory header, each file has 7 columns with the following data: </p> <ul> <li>time, <em>t U<sub>∞</sub>/c</em></li> <li>cl: lift coefficient, <em>c<sub>l</sub></em></li> <li>cd: drag coefficient, <em>c<sub>d</sub></em></li> <li>cm: coefficient of moments with respect to c/4, <em>c<sub>m</sub></em></li> <li>dcl: perturbation of <em>c<sub>l</sub></em> with respect to steady state value, ∆<em>c<sub>l</sub></em> </li> <li>dcd: perturbation of <em>c<sub>d</sub></em> with respect to steady state value, ∆<em>c<sub>d</sub></em> </li> <li>dcm: perturbation of <em>c<sub>m</sub></em> with respect to steady state value, ∆<em>c<sub>m</sub></em> </li> </ul> <p>Reference time (t=0) is taken as the time at which the center of the vortical gust reaches the position of the leading edge of the airfoil (if advected at a velocity <em>U<sub>∞</sub></em>). <br> <br> <strong>Nomenclature </strong><br> The names of the files will follow the acronym t_AaYyDdVv.txt, where the lowecase letters are placeholders for: </p> <table> <tbody> <tr> <td> t </td> <td> Type of vortical gust</td> <td> T: Taylor, LO: Lamb-Oseen</td> </tr> <tr> <td> a </td> <td> Angle of attack </td> <td><em> α</em> = [+8,0,-8] deg</td> </tr> <tr> <td> y </td> <td> Initial vertical position of the centre of the vortex</td> <td><em> h/c </em>= [0,0.5,1]</td> </tr> <tr> <td> d </td> <td> Diameter of the core of the vortex </td> <td><em> D/c </em>= [0.5,1,2]</td> </tr> <tr> <td> v </td> <td> Circumferential velocity </td> <td><em> v<sub>0m</sub></em>/<em>U<sub>∞</sub></em> = [0.1,0.3,1]</td> </tr> </tbody> </table>
SGS-LTER Standard Production Data: 1983-2008 Annual Aboveground Net Primary Production on the Central Plains Experimental Range, Nunn, Colorado, USA 1983-2008, ARS Study Number 6 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/700/1. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. The objective of the long-term ANPP study is to monitor long-term net above ground primary production of the shortgrass steppe community by species. There are 6 sites: ridgetop (ridge), midslope (mid), swale, ESA (replicate 1 not 2), Section 25 (SEC 25), and owl-creek (OC). Each site is located in a different landscape position or soil type on the shortgrass steppe and may be grazed or not. Ridgetop, midslope and swale are grazed and are sampled along a catena. Section 25 is grazed and is located in an upload grassland. ESA is an ungrazed upland grassland an is the control from the Ecosystem Stress Area experiment. Owl Creek is ungrazed and is located in the lowland along the owl creek drainage. There are 3 transects with 5 plots in each transect. Plots in the grazed locations are protected by cages. Because this is a monitoring effort, true replicates across the landscape are not
SGS-LTER Long-Term Monitoring Project: Vegetation Cover on Small Mammal Trapping Webs on the Central Plains Experimental Range, Nunn, Colorado, USA 1999 -2006, ARS Study Number 118 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/140/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83458. The abundance and diversity of small mammals in shortgrass steppe is strongly influenced by the structure and composition of vegetation. Vegetation structure provides cover from predators and harsh abiotic conditions. Plant species composition affects the types of seeds and herbaceous material available to granivores and herbivores, and influences arthropod populations, which are important prey for the omnivorous species that dominate in shortgrass steppe. Both vegetation structure and plant community composition are sensitive to the availability of precipitation as well as the activity of large mammalian herbivores. In 1999, we began measuring vegetation structure and plant community composition on the three grassland and three shrubland trapping webs where we live-trap small mammals
SGS-LTER Long-term Monitoring Project: Spotlight Rabbit Count on the Central Plains Experimental Range, Nunn, Colorado, USA 1994-2006, ARS Study Number 98 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/136/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83448. Rabbits are the most important small-mammal herbivores in shortgrass steppe, and may significant influence the physiognomy and population dynamics of herbaceous plants and woody shrubs. Rabbits also are the most important prey of mammalian carnivores such as coyotes and large raptors such as golden eagles and great horned owls. Two hares (Lepus californicus, L. townsendii) and one cottontail rabbit (Sylvilagus audubonii) occur in shortgrass steppe. In 1994, we initiated long-term studies to track changes in relative abundance of rabbits on the Central Plains Experimental Range (CPER). On four nights each year (one night each season, usually on new moon nights in January, April, July, October), we drove a 32-km route consisting of pasture two-track and gravel roads on the CPER. This wa
SGS-LTER Long-Term Montioring Project: Arthropod Pitfall Trapping on Small Mammal Trapping Webs on the Central Plains Experimental Range, Nunn, Colorado, USA 1998-2006, ARS Study Number 118 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/134/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83450. With the exception of heteromyids, eg kangaroo rats and pocket mice, most small rodents in shortgrass steppe are omnivorous. Depending on season, arthropods (insects and arachnids) make up 40-85% of the diet of grasshopper mice and thirteen-lined ground squirrels, the most widespread rodents in northern shortgrass steppe. Small mammals are among the most important predators of ground-dwelling macroarthropods and herbivorous insects provide a direct resource link between weather and plant production. Understanding temporal variability in the abundance of arthropods is central to determining the mechanisms that drive small rodent populations. At present, there are no long-term studies of arthropods in shortgrass steppe, despite the important role that these taxa play in grassland food w
SGS-LTER Long-Term Monitoring Project: Small Mammals on Trapping Webs on the Central Plains Experimental Range, Nunn, Colorado, USA 1994 -2006, ARS Study Number 118 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/137/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83452. Small mammals (rabbits, rodents) are integral components of semiarid ecosystems because of their roles as consumers of plants, seeds and arthropods, as soil disturbance agents, and as food for raptors, snakes and mammalian carnivores. Because of their vagility and intermediate trophic position, populations of small mammals may track changes in vegetation and the abiotic environment that may result from shifts in land-use and other anthropogenic disturbances. However, these populations are variable over space and time, and their response to environmental changes may not be immediately apparent given their behavioral flexibility and relatively long life-spans and generation times. Patterns in the distribution and abundance of small mammals thus may simultaneously reflect and affect the
SGS-LTER Ecosystem Stress Area - long-term density dataset following nutrient enrichment stress on the Central Plains Experimental Range in Nunn, Colorado, USA 1975-2011, ARS Study Number 3 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/520/8. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Water, nitrogen, and water-plus-nitrogen at levels beyond the range normally experience by shortgrass steppe communities were applied from 1971 through 1975, plant densities were sampled through 1977, and then sampling resumed in 1982, with sampling frequencies changing from annually to every other year. The initial sampling from 1970 to 1974 showed that the water and water plus nitrogen treatments had the strongest effect on plant community structure, both treatments increased biomass, and exotic weed species were noted on the water plus nitrogen treatment. Later sampling from 1982 to 1991 showed a ten-fold increase in exotic weed species on the water plus nitrogen plots as compared to the controls (Milchunas and Lauenroth 1995), a community change that has persisted on this site due to a chronic elevation of soil nitrogen caused by a plant tissue/soil organic matter feedback mec
SGS-LTER Ecosystem Stress Area - long-term point-frame (percent basal cover) dataset following nutrient enrichment stress on the Central Plains Experimental Range in Nunn, Colorado, USA 1982-2011, ARS Study Number 3 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/521/7. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Water, nitrogen, and water-plus-nitrogen at levels beyond the range normally experience by shortgrass steppe communities were applied from 1971 through 1975, plant densities were sampled through 1977, and then sampling resumed in 1982, with sampling frequencies changing from annually to every other year. The initial sampling from 1970 to 1974 showed that the water and water plus nitrogen treatments had the strongest effect on plant community structure, both treatments increased biomass, and exotic weed species were noted on the water plus nitrogen treatment. Later sampling from 1982 to 1991 showed a ten-fold increase in exotic weed species on the water plus nitrogen plots as compared to the controls (Milchunas and Lauenroth 1995), a community change that has persisted on this site due to a chronic elevation of soil nitrogen caused by a plant tissue/soil organic matter feedback mec
CBP01 Variable distance line-transect sampling of bird population numbers in different habitats on Konza Prairie (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-knz/26/11. The abstract below was extracted from the Level 0 data package and is included for context: Records of bird species based on line transect sampling, giving perpendicular distance of sighting from the transect line on 16 separate transects. Bird surveys were conducted 2-4 times per year in January, April, June, and October for a 29-year period from 1981 to 2009. Transects were designed to determine bird communities and population numbers associated with tallgrass prairie habitats with different experimental treatments (fire frequency, grazed by bison vs. ungrazed), riparian habitats on forest edge, and gallery forests dominated by oak woodland.
Accession numbers for radiocarbon and stable carbon isotopes of dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) in soil leachates from permafrost soils collected from the North Slope of Alaska in the summers of 2018 and 2022
Leachates of dissolved organic carbon (DOC) from permafrost soils were prepared from soils collected from the North Slope of Alaska in 2018 and 2022. Soil leachates were then either kept in the dark or exposed to light from LEDs at 305 nm (UV) and 405 nm (visible), and then inoculated with native microbial communities and incubated. At the start of the biological incubations, single replicates of the DOC after dark or light treatment and inoculation were assigned accession numbers and analyzed for 14C and 13C at the National Ocean Sciences Accelerator Mass Spectrometry (NOSAMS) facility. At the end of the biological incubations, duplicates of the dissolved inorganic carbon (DIC) in those waters were assigned accession numbers and analyzed for 14C and 13C at the NOSAMS facility.
CSM06 Seasonal summary of numbers of small mammals on miscellaneous traplines in prairie habitats that were trapped from 1 to 11 years at Konza Prairie
Data set contains seasonal summaries (spring, summer and autumn) of the number of individuals of each species of small mammal captured (relative abundance) on each prairie trapline. Each record contains year, season, trapline and number of individuals captured of each species. These live trap records are based on daily captures during 4-day trapping periods in spring (early March to early April), summer (late June to late July) and autumn (early October to mid-November) for each permanent trapline (two traplines per treatment). These treatments include annual burns, 2-year burns, 4-year burns and 10-year burns; none were grazed by bison. This data set includes 14 traplines sampled in autumn and spring and 30 traplines in summer.
CSM05 Seasonal summary of numbers of small mammals on the six LTER traplines in prairie habitats on which fire regime has been reversed at Konza Prairie
Data set contains seasonal summaries (spring and autumn) of the number of individuals of each species of small mammal captured (relative abundance) on each grassland trapline. Each record contains year, season, trapline and number of individuals captured of each species. These live trap records are based on daily captures during a single 4-day trapping period in spring (mid-March to early April) and autumn (late October to early December) for each of six permanent traplines established on two fire treatments (three traplines per treatment). These two fire treatments include one treatment that was changed from a 20-year burn to an annual burn and one that was changed from an annual burn to 20 years between fires. Bison do not graze these two habitat types.
CSM03 Seasonal summary of numbers of small mammals on the two LTER traplines in planted grassland (Brome fields) habitats at Konza Prairie
Data set contains seasonal summaries (spring, summer and autumn) of the number of individuals of each species of small mammal captured (relative abundance) on each woodland trapline. Each record contains year, season, trapline and number of individuals captured of each species. These live trap records are based on daily captures during a single 4-day trapping period in spring (early March to early April), summer (early July to late July) and autumn (mid-October to early December) for each of four permanent traplines established in two habitats (two traplines in gallery forest and two on limestone ledges). Bison did not graze any of the treatment units during the period of study.
Shrimp populations variability in numbers and sizes in response to disturbance and seasons on 20 pools along the reach of Quebrada Prieta, Luquillo Experimental Forest
Shrimp populations were monitored at approximately 3 week intervals to determine the variability in numbers and sizes of each species in response to disturbance and seasons. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Spatial and temporal differences in shrimp numbers (1 year, 20 pools)
We added woody debris to stream pools in three streams in an experiment designed to increase cover for freshwater shrimp. We trapped four species of freshwater shrimp during 4 months following wood additions. Stream pool morphology was estimated using maximum depth, surface area, and volume. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Adelie penguin diet composition, fish species and number, 1991-2024
The fundamental long-term objective of the seabird component of the Palmer LTER (PAL) has been to identify and understand the mechanistic processes that regulate the mean fitness (population growth rate) of regional penguin populations. Since the inception of PAL, Adélie penguin populations have effectively collapsed, gentoo penguin populations have increased dramatically and chinstrap penguin populations have remained relatively stable. These trends are spatially and temporally coherent with regional warming and decreasing sea ice duration. Adélie penguins are an ice-obligate polar species whose life history is intimately linked to the presence of sea ice, while chinstrap and gentoo penguins are ice-intolerant species whose life histories evolved in the sub-Antarctic, where sea ice is a less permanent feature of the marine ecosystem. The PAL study region includes five main islands on which Adélie penguin colonies have historically occurred, with each island containing a different number of spatially segregated sub-colonies. These colonies are censused to determine the total number of nests and chicks produced each year, and breeding success. Diet samples are acquired to understand diet composition (e.g., krill, fish) and krill length-frequencies. In general, krill constitute the most important component of the summer diets by mass of these three penguin species, but changes in PAL krill abundances have exhibited no long-term trends and thus far, have failed to explain the divergent patterns in penguin populations evident in our time series. Chick fledging masses are recorded as a cumulative measure of climate, weather, diet, and parental influences on chick health at the end of the breeding season. These data have provided valuable insights into the marine and terrestrial factors that influence Adélie penguin population fitness. No data were collected during the 2021-2022 season due to the Palmer Station pier rebuild.
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Raw read counts and phased SNP counts for every single cell in the sequencing datasets of the breast cancer patient S1 from "Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL"
<p>This dataset contains the raw read counts and phased SNP counts for every single cell in the sequencing datasets of breast cancer patient S1 from “Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL” [Zaccaria & Raphael, 2020]. These data enable the full reproduction of all the results in the related manuscript for breast cancer patient S1. Specifically, the data are provided in two files for every dataset <em>DAT</em> of patient S1 with the following format:</p> <ol> <li><em>DAT.raw</em>_<em>read</em>_<em>counts.bed.gz </em>is a multi-cell BED file containing the raw read counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>START: the starting genomic position of a genomic bin in the chromosome</li> <li>END: the ending genomic position of the genomic bin in the chromosome</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>NORMAL: the raw read count for the specified bin from a matched-normal sample</li> <li>COUNT: the raw read count for the specified bin in the specified cell</li> <li>RDR: the estimated read-depth ratio for the specified bin in the specified cell</li> </ul> </li> <li><em>DAT.phased</em>_<em>snps</em>_<em>counts.pos.gz </em>is a multi-cell POS file containing the phased SNP counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>POS: the genomic position in the chromosome of a germline SNP</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>COUNT_HAPLOTYPE_A: the count of reads that cover the SNP and that belong to haplotype A in the specified cell</li> <li>COUNT_HAPLOTYPE_B: the count of reads that cover the SNP and that belong to haplotype B in the specified cell</li> </ul> </li> </ol> <p>All the files have been compressed using standard <em>gzip</em>.</p>
Raw read counts and phased SNP counts for every single cell in the sequencing datasets of the breast cancer patient S0 from "Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL"
<p>This dataset contains the raw read counts and phased SNP counts for every single cell in the sequencing datasets of breast cancer patient S0 from “Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL” [Zaccaria & Raphael, 2020]. These data enable the full reproduction of all the results in the related manuscript for breast cancer patient S0. Specifically, the data are provided in two files for every dataset <em>DAT</em> of patient S0 with the following format:</p> <ol> <li><em>DAT.raw</em>_<em>read</em>_<em>counts.bed.gz </em>is a multi-cell BED file containing the raw read counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>START: the starting genomic position of a genomic bin in the chromosome</li> <li>END: the ending genomic position of the genomic bin in the chromosome</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>NORMAL: the raw read count for the specified bin from a matched-normal sample</li> <li>COUNT: the raw read count for the specified bin in the specified cell</li> <li>RDR: the estimated read-depth ratio for the specified bin in the specified cell</li> </ul> </li> <li><em>DAT.phased</em>_<em>snps</em>_<em>counts.pos.gz </em>is a multi-cell POS file containing the phased SNP counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>POS: the genomic position in the chromosome of a germline SNP</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>COUNT_HAPLOTYPE_A: the count of reads that cover the SNP and that belong to haplotype A in the specified cell</li> <li>COUNT_HAPLOTYPE_B: the count of reads that cover the SNP and that belong to haplotype B in the specified cell</li> </ul> </li> </ol> <p>All the files have been compressed using standard <em>gzip</em>.</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.