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These laser altimetry data were collected as part of the 2023-24 <a href="https://www.coldex.org">NSF COLDEX </a> CXA2 airborne campaign targeting the southern flank of East Antarctica's Dome A. In this Level 2 product, we have used the laser range to the surface and complementary aircraft position data to calculated the ice surface elevation, which is an important constraint on ice flow. Complementary radar, gravity, magnetics and imagery were also collected. <p> <i>Data format:</i>Data are formatted as text files with a header and the following tab delimited format columns. Data are in the same format as similar <a href="https://doi.org/10.5067/JV9DENETK13E"> IceBridge ILUTP2 altimetry data. </a> <p> Field 1: Year (UTC)<br> Field 2: Day of year (UTC)<br> Field 3: Second of day (UTC)<br> Field 4: Longitude Angle (deg) (WGS-84) <br> Field 5: Latitude Angle (deg) (WGS-84)<br> Field 6: Laser Derived Surface Elevation (m) (WGS-84)<br> <p> Missing values have been replaced by "nan". The effective footprint of the laser data is 25 m along track by 1 meter across track. Some cloud filtering was performed. <p> <i>Uncertainties</i>: A comparison of this laser altimetry dataset north of 87.5˚S with the <a href="https://doi.org/10.7910/DVN/EBW8UC"> REMAv2 </a>100 m mosaic digital terrain model indicate a median bias of 17 cm and a root mean squared (RMS) difference of 20 cm. Intersections between profiles within this survey, on the Antarctic Plateau but away from South Pole Station, have RMS differences of 6.8 cm. <p> <i>Datum: </i>WGS-84 ellipsoid; ITRF 2008 <p> <i>Geolocation: </i>Positioning and orientation for CXA1 came from loosely coupled joint PPP/inertial solutions using a Novatel OEM-4 GPS receiver and an iMAR FSAS IMU. <p> <i>Pointing bias: </i> roll: 0.340 degrees; pitch: -0.505 degrees <br> Pointing angle (pointing bias) is the angular offset of the downward-pointing laser boresight respect to the vehicle body frame's vertical (Z) axis. This estimated angle is derived by comparing measurements at crossovers. Pointing angle is provided in the vehicle body frame, using the laser origin for the rotation node. A positive pitch rotation indicates that the laser beam intersects the ground forward of the z-axis. A positive roll rotation indicates that the laser beam intersects the ground left of the z-axis. Pointing biases were found using the minimization of cross over difference method from <a href="http://dx.doi.org/10.3189/2015JoG14J048">Young et al., 2015</a>. <p> <i>Level arm: </i>X: 0 m; Y: 0.2 m; Z: -0.22 m <br> The lever arm is the position of the laser origin relative to the aircraft position solution, estimated using crossover-error minimization. Lever arm is provided in the vehicle body frame, with +X is forward, +Y is right, and +Z is down. Lever arm was measured after installation in the field. <p> <i>GNSS_antenna: </i>AeroAntenna AT1675-17W-TCNF-000-RG-36-NM <br> The coordinate system for the laser-gps lever arm is X forward, Y right, and Z down, from the center of position.
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Data from: Inheritance of DNA methylation differences in the mangrove Rhizophora mangle
{"Abstract":["This record contains supplementary information for the article "Inheritance of DNA methylation differences in the mangrove Rhizophora mangle" published in Evolution&Development. It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. Short reads are available on SRA (PRJNA746695). Note that demultiplexing of the pooled reads (SRX11452376) will fail because the barcodes are already removed and the header information is lost during SRA submission. Instead, use the pre-demultiplexed reads that are as well linked to PRJNA746695.<\/p>\n\n\n <\/p>\n\nTable S13 (TableS13_DSSwithGeneAnnotation.offspringFams.csv.gz): <\/strong><\/p>\n\nDifferential cytosine methylation between families using the mother data set. The first three columns fragment number ("chr"), the position within the fragment ("pos"), and the sequence context ("context"). Columns with the pattern FDR_<X>_vs_<Y> contain false discovery rates of a test comparing population X with population Y. Average DNA methylation levels for each population are given in the columns "AC", "FD", "HI", "UTB", "WB", and "WI". The remaining columns contain the annotation of the fragment, for example whether it matches to a gene and if yes, the gene name ID and description are provided.<\/p>"]}
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- Award ID(s):
- 1930451
- PAR ID:
- 10384317
- Publisher / Repository:
- Zenodo
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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These laser altimetry data were collected as part of the 2022-23 <a href="https://www.coldex.org">NSF COLDEX </a> CXA1 airborne campaign targeting the southern flank of East Antarctica's Dome A. In this Level 2 product, we have used the laser range to the surface and complementary aircraft position data to calculated the ice surface elevation, which is an important constraint on ice flow. Complementary radar, gravity, magnetics and imagery were also collected. <p> <i>Data format:</i>Data are formatted as text files with a header and the following tab delimited format columns. Data are in the same format as similar <a href="https://doi.org/10.5067/JV9DENETK13E"> IceBridge ILUTP2 altimetry data. </a> <p> Field 1: Year (UTC)<br> Field 2: Day of year (UTC)<br> Field 3: Second of day (UTC)<br> Field 4: Longitude Angle (deg) (WGS-84) <br> Field 5: Latitude Angle (deg) (WGS-84)<br> Field 6: Laser Derived Surface Elevation (m) (WGS-84)<br> <p> Missing values have been replaced by "nan". The effective footprint of the laser data is 25 m along track by 1 meter across track. Some cloud filtering was performed. <p> <i>Uncertainties</i>: A comparison of this laser altimetry dataset north of 87.5˚S with the <a href="https://doi.org/10.7910/DVN/EBW8UC"> REMAv2 </a>100 m mosaic digital terrain model indicate a median bias of 17 cm and a root mean squared (RMS) difference of 20 cm. Intersections between profiles within this survey, on the Antarctic Plateau but away from South Pole Station, have RMS differences of 6.4 cm. <p> <i>Datum: </i>WGS-84 ellipsoid; ITRF 2008 <p> <i>Geolocation: </i>Positioning and orientation for CXA1 came from loosely coupled joint PPP/inertial solutions using a Novatel OEM-4 GPS receiver and an iMAR FSAS IMU. <p> <i>Pointing bias: </i> roll: -0.2 degrees; pitch: -0.350 degrees <br> Pointing angle (pointing bias) is the angular offset of the downward-pointing laser boresight respect to the vehicle body frame's vertical (Z) axis. This estimated angle is derived by comparing measurements at crossovers. Pointing angle is provided in the vehicle body frame, using the laser origin for the rotation node. A positive pitch rotation indicates that the laser beam intersects the ground forward of the z-axis. A positive roll rotation indicates that the laser beam intersects the ground left of the z-axis. Pointing biases were found using the minimization of cross over difference method from <a href="http://dx.doi.org/10.3189/2015JoG14J048">Young et al., 2015</a>. <p> <i>Level arm: </i>X: 0 m; Y: 0.2 m; Z: -0.22 m <br> The lever arm is the position of the laser origin relative to the aircraft position solution, estimated using crossover-error minimization. Lever arm is provided in the vehicle body frame, with +X is forward, +Y is right, and +Z is down. Lever arm was measured after installation in the field. <p> <i>GNSS_antenna: </i>AeroAntenna AT1675-17W-TCNF-000-RG-36-NM <br> The coordinate system for the laser-gps lever arm is X forward, Y right, and Z down, from the center of position.more » « less
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Abstract We present the first long-read de novo assembly and annotation of the luna moth (Actias luna) and provide the full characterization of heavy chain fibroin (h-fibroin), a long and highly repetitive gene (>20 kb) essential in silk fiber production. There are >160,000 described species of moths and butterflies (Lepidoptera), but only within the last 5 years have we begun to recover high-quality annotated whole genomes across the order that capture h-fibroin. Using PacBio HiFi reads, we produce the first high-quality long-read reference genome for this species. The assembled genome has a length of 532 Mb, a contig N50 of 16.8 Mb, an L50 of 14 contigs, and 99.4% completeness (BUSCO). Our annotation using Bombyx mori protein and A. luna RNAseq evidence captured a total of 20,866 genes at 98.9% completeness with 10,267 functionally annotated proteins and a full-length h-fibroin annotation of 2,679 amino acid residues.more » « less
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Ingvarsson, P (Ed.)Abstract Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70–90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.more » « less
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{"Abstract":["The intended use of this archive is to facilitate meta-analysis of the Data Observation Network for Earth (DataONE, [1]). <\/p>\n\nDataONE is a distributed infrastructure that provides information about earth observation data. This dataset was derived from the DataONE network using Preston [2] between 17 October 2018 and 6 November 2018, resolving 335,213 urls at an average retrieval rate of about 5 seconds per url, or 720 files per hour, resulting in a data gzip compressed tar archive of 837.3 MB . <\/p>\n\nThe archive associates 325,757 unique metadata urls [3] to 202,063 unique ecological metadata files [4]. Also, the DataONE search index was captured to establish provenance of how the dataset descriptors were found and acquired. During the creation of the snapshot (or crawl), 15,389 urls [5], or 4.7% of urls, did not successfully resolve. <\/p>\n\nTo facilitate discovery, the record of the Preston snapshot crawl is included in the preston-ls-* files . There files are derived from the rdf/nquad file with hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f . This file can also be found in the data.tar.gz at data/8c/67/e0/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f/data . For more information about concepts and format, please see [2]. <\/p>\n\nTo extract all EML files from the included Preston archive, first extract the hashes assocated with EML files using:<\/p>\n\ncat preston-ls.tsv.gz | gunzip | grep "Version" | grep -v "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep "hash://" | sort | uniq > eml-hashes.txt<\/p>\n\nextract data.tar.gz using:<\/p>\n\n~/preston-archive$$ tar xzf data.tar.gz <\/p>\n\nthen use Preston to extract each hash using something like:<\/p>\n\n~/preston-archive$$ preston get hash://sha256/00002d0fc9e35a9194da7dd3d8ce25eddee40740533f5af2397d6708542b9baa\n<eml:eml xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml_1.1" packageId="doi:10.18739/A24P9Q" system="https://arcticdata.io" scope="system" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.1 ~/development/eml/eml.xsd">\n <dataset>\n <alternateIdentifier>urn:x-wmo:md:org.aoncadis.www::d76bc3b5-7b19-11e4-8526-00c0f03d5b7c</alternateIdentifier>\n <alternateIdentifier>d76bc3b5-7b19-11e4-8526-00c0f03d5b7c</alternateIdentifier>\n <title>Airglow Image Data 2011 4 of 5</title>\n...<\/p>\n\nAlternatively, without using Preston, you can extract the data using the naming convention:<\/p>\n\ndata/[x]/[y]/[z]/[hash]/data<\/p>\n\nwhere x is the first 2 characters of the hash, y the second 2 characters, z the third 2 characters, and hash the full sha256 content hash of the EML file.<\/p>\n\nFor example, the hash hash://sha256/00002d0fc9e35a9194da7dd3d8ce25eddee40740533f5af2397d6708542b9baa can be found in the file: data/00/00/2d/00002d0fc9e35a9194da7dd3d8ce25eddee40740533f5af2397d6708542b9baa/data . For more information, see [2].<\/p>\n\nThe intended use of this archive is to facilitate meta-analysis of the DataONE dataset network. <\/p>\n\n[1] DataONE, https://www.dataone.org\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . DataONE was crawled via Preston with "preston update -u https://dataone.org".\n[3] cat preston-ls.tsv.gz | gunzip | grep "Version" | grep -v "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep -v "hash://" | sort | uniq | wc -l\n[4] cat preston-ls.tsv.gz | gunzip | grep "Version" | grep -v "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep "hash://" | sort | uniq | wc -l\n[5] cat preston-ls.tsv.gz | gunzip | grep "Version" | grep "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep -v "hash://" | sort | uniq | wc -l<\/p>\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.<\/p>"]}more » « less
