Kantor, Rose · Shakya, Migun · Ruth, Nelson · et al.
2,095 rows · 907 KB · fasta, tsv
A virus genome database representing 21,015 near-complete virus genomes collected from untargeted ultra-deep RNA/DNA combined sequencing of wastewater. Sequence data was provided by the CASPER consortium and raw data may be found on NCBI SRA under bioprojects PRJNA1247874 and PRJNA1198001. Data underwent read trimming, rRNA and human read removal, de novo assembly, and selection of high-quality viral contigs. Contigs were clustered at 95% identity and 85% query coverage to dereplicate. Chimera-checking required at least two independent assemblies of the same viral genome or presence of the genome in another reference database. Annotation made use of RdRpCATCH, geNomad, checkV, BLASTN against NCBI core-nt, and RNAVirHost. The RdRp fasta files contain representative RdRp sequences identified through homology to major RdRp reference databases and clustered at 90% sequence identity over 75% sequence coverage. Included sequences contain all three conserved RdRp motifs (A, B, and C) arranged in either the canonical ABC configuration or the permuted CAB configuration.
Hubbard, Alfred · Solares, Edwin · Hemming-Schroeder, Elizabeth
88 rows · 18 KB · fasta
These are the files needed to run the Broad Institute's malaria amplicon pipeline for the PvGAP Plasmodium vivax panel, described in detail here . They consist of FASTA files containing the forward and reverse primers and another FASTA file containing reference sequences for each target, derived from the PvP01 reference genome.
This dataset supports the findings of the manuscript "Root anatomical traits modulate the assembly and nitrogen transformation potential of root-associated microbiomes in a temperate steppe" (NPH-MS-2026-55667). It contains root traits data, bacterial 16S rRNA gene absolute abundances, functional genes relative abundances, DNA extraction metadata, and phylogenetic marker sequences for 37 plant species from a temperate steppe ecosystem. The dataset includes the following files: 1. root traits.csv - Root traits including average diameter (AD), specific root length (SRL), specific root area (SRA), root tissue density (RTD), root nitrogen content (RNC), root carbon content (RCC), carbon‑nitrogen ratio (RCN), cortex layer number (CLN), cortex thickness (CT), and the ratio of cortex thickness to root diameter (CTRD). The first column lists plant species names. 2. Absolute abundance of 16S rRNA gene.csv - Quantitative PCR (qPCR) derived absolute abundances of bacterial 16S rRNA gene copies (copies/ng DNA) across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 3. DNA extraction sample weight.csv - Fresh weight (grams) of root material used for DNA extraction for each sample, linked by SampleID to the abundance data. 4. DNA extraction concentration.csv - Qubit‑measured DNA concentrations (ng/μL) and the sample volume (μL) used for quality control, together with sample metadata. 5. 37species.fasta - DNA sequences of two chloroplast markers (matK and rbcL) for the 37 plant species included in the study. The sequences are in FASTA format with headers formatted as ">Species". These were used for host phylogeny construction and Pagel's λ analyses. 6. Quantitative PCR results of functional gene.csv - Quantitative PCR (qPCR) derived relative abundances of bacterial 16S rRNA gene and functional genes across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 7. README.md - A detailed description of each file, column headers, abbreviations, units, and any missing value codings (NA). All data are provided to ensure transparency and reproducibility of the analyses. For methodological details, please refer to the Materials and Methods section of the associated publication. These data are under embargo until the associated research article is published. After that date, they will be freely available under a Creative Commons Attribution 4.0 International (CC BY 4.0) license. During the embargo period, the metadata (title, authors, abstract) and the DOI remain publicly visible, but the data files are not accessible. For access requests before the embargo expires, please contact the corresponding author.
NOAA Coral Reef Watch (v3.1 CoralTemp) Daily Global 5km Satellite Sea Surface Temperature Anomaly. This is a product of NOAA Coral Reef Watch Daily Global 5km Satellite Coral Bleaching Heat Stress Monitoring Product Suite cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature_anomaly (degree_C) mask (pixel characteristics flag array, pixel_classification)
7-day average sea surface temperature (SST) from the AVHRR and VIIRS instruments aboard the NOAA and MetOp satellites, 2006-present, is generated by NOAA/NESDIS/STAR using the Advanced Clear-Sky Processor for Oceans (ACSPO) processing system. Only nighttime overpasses are used and composited into daily mean grids (~830 m), then the daily composite grids are averaged into gridded 7-day temperature averages. More info: https://eastcoast.coastwatch.noaa.gov/cw_avhrr-viirs_sst.php cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (sea_surface_subskin_temperature, degree_C)
Climatological 7-day average sea surface temperature (SST) from 2007 to 2025, i.e. there are 52 7-day periods each representing a 2007-2025 mean SST for that period. The 18-year period for averaging begins May 21, 2007 and ends May 20, 2025. Data are merged from the AVHRR and VIIRS instruments aboard the NOAA and MetOp satellites. SST is generated by NOAA/NESDIS/STAR using the Advanced Clear-Sky Processor for Oceans (ACSPO) processing system. Only nighttime overpasses are used and composited into daily mean grids (~830 m), then the daily composite grids are averaged into gridded 7-day temperature averages. Finally, the 18-year climatological average for each 7-day period is averaged from the 7-day files. More info: https://eastcoast.coastwatch.noaa.gov/cw_avhrr-viirs_sst.php cdm_data_type = Grid VARIABLES (all of which use the dimensions [sevenDayPeriodOfYear][level][latitude][longitude]): sst (sea_surface_subskin_temperature, degree_C)
Jet Propulsion Laboratory data from a local source. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (Analysed SST with land and ice masks applied, degree_C)
Jet Propulsion Laboratory SST MUR data from a local source. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (Analysed SST with land and ice masks applied, degree_C)
Jet Propulsion Laboratory data from a local source. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (Analysed SST with land and ice masks applied, degree_C)
NOAA Coral Reef Watch Daily (v3.1) Global 5km Satellite Sea Surface Temperature (CoralTemp). CoralTemp is derived from three different but related 5km daily gap-free SST data sets and provides an internally consistent SST product that stretches from 1985 to present: Operational Sea Surface Temperature and Sea Ice Analysis (OSTIA) Sea Surface Temperature Reanalysis (1985-2002), Geo-Polar Blended Night-only Sea Surface Temperature Reanalysis (2002-2016), Geo-Polar Blended Night-only Sea Surface Temperature Near Real-Time (2017 to present). cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): analysed_sst (analysed sea surface temperature, degree_C) sea_ice_fraction (1)
Sea surface temperature retrievals produced by NOAA/NESDIS/Office of Satellite and Product Operations (OSPO) office from Visible and Infrared Imager/Radiometer Suite (VIIRS) sensor cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][altitude][rows][cols]): l2p_flags swath_latitude (Latitude, degrees_north) swath_longitude (Longitude, degrees_east) sea_surface_temperature (sea surface subskin temperature, degree_C) sses_bias (SSES bias estimate, degree_C) sses_standard_deviation (degree_C) graphics (graphics overlay planes)
Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, degree_C) sses_bias (SSES bias estimate, kelvin) sses_standard_deviation (kelvin) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)
Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, kelvin) sses_bias (SSES bias estimate, kelvin) sses_standard_deviation (kelvin) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)
Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, kelvin) sses_bias (SSES bias estimate, kelvin) sses_standard_deviation (kelvin) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)
Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, degree_C) sses_bias (SSES bias estimate, degree_C) sses_standard_deviation (degree_C) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)
This is a product of NOAA Coral Reef Watch Global 5km Satellite Coral Bleaching Heat Stress Monitoring Product Suite, derived from CoralTemp v1.0. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (analysed sea surface temperature, degree_C) mask (Pixel characteristics flag array, pixel_classification) sea_surface_temperature_anomaly (degree_C)
This is a product of NOAA Coral Reef Watch Global 5km Satellite Coral Bleaching Heat Stress Monitoring Product Suite, derived from CoralTemp v1.0. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (analysed sea surface temperature, degree_C) mask (Pixel characteristics flag array, pixel_classification) sea_surface_temperature_anomaly (degree_C)
A daily Sea Surface Temperature (SST) Anomaly product created by ERD based on JPL MUR's climatology (2003-2014) of the Jet Propulsion Laboratory's (JPL) Multi-scale Ultra-high Resolution (MUR), merged, multi-sensor L4 v4.1 Foundation SST analysis product (part of the Group for High-Resolution Sea Surface Temperature (GHRSST) project). The data for the most recent 4 days is usually revised everyday. The data for other days is sometimes revised. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sstAnom (sea surface temperature anomaly, degree_C) mask (sea/land field composite mask)