Find research datasets worth reusing

Azimuth ATAC Reference - Human PBMC

Here we provide the reference data files used to run the Azimuth ATAC Human PBMC reference web application. For a full description of the reference data structure, please see the wiki at <a href="https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format">https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format</a>.

Azimuth ATAC Reference - Human BMMC

Here we provide the reference data files used to run the Azimuth ATAC Human BMMC reference web application. For a full description of the reference data structure, please see the wiki at <a href="https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format">https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format</a>.

Azimuth Reference - Human Liver

Here we provide the reference data files used to run the Azimuth Human Liver reference web application. For a full description of the reference data structure, please see the wiki at <a href="https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format">https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format</a>.

FRGMRC - FIRST Radio Galaxy Morphology Reference Catalogue

FRGMRC - FIRST Radio Galaxy Morphology Reference Catalogue - Version 1.0 Brand et al. 2023 - <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.522..292B/abstract">https://ui.adsabs.harvard.edu/abs/2023MNRAS.522..292B/abstract</a>

Additional annotation, alignment, and results from Ka/Ks analysis for Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus)

Annotation files, alignments, and results summaries from Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus). Pairwise genome alignments contain the .maf suffix FASTA alignments from stitched gene blocks contain the .fasta suffix CSV file containing the Ka/Ks results RepeatMasker .out file

openmit-licenseMar 2022View details →

Reference data from the Pathomove simulation, for the manuscript "Novel pathogen introduction triggers rapid evolution in animal social movement strategies"

This is a reference dataset of multiple runs of the 'Pathomove' simulation, to accompany the manuscript "Novel pathogen introduction rapidly alters the evolution of movement, restructuring animal societies". The datasets are in the form of R data objects saved as Rds files. This version of the data is intended to accompany a resubmission to eLife.

opencc-by-4.0Apr 2023View details →

Large-eddy simulation source code and data for (LS)2D reference publication in JAMES.

This archive contains the MicroHH large-eddy simulation source code, the (LS)2D source code, and all simulation input and statistics, used for the publication: "The Benefits and Challenges of Downscaling a Global Reanalysis with Doubly-Periodic Large-Eddy Simulations" by B.J.H. van Stratum et al.

opencc-by-4.0Dec 2021View details →

CMIP6 derived ensemble of global vapor pressure deficit, potential evapotranspiration, and reference evapotranspiration

Climate change induced trends in long-term aridity—via changes to atmospheric water demand for have the potential to impact surface water availability across the globe by altering efficiency by which precipitation is converted to runoff. Quantification of aridity requires estimates of evaporative demand, often using vapor pressure deficit, potential evapotranspiration, and/or reference evapotranspiration, but no comprehensive estimate of these climate variables exists to date from the Coupled Model Intercomparison Project 6 (CMIP6). Here we present global monthly estimates of the Penman-Monteith short grass reference evapotranspiration, its advective and radiation components, Priestley-Taylor potential evapotranspiration, and vapor pressure deficit from 16 CMIP6 general circulation models (GCM) for the historical period and four future emission scenarios ranging from low to high projected emissions. The purpose of this dataset is to offer structured and well-documented estimates of historical and future projected evaporative demand derived from the state-of-the-science CMIP6 climate models for use in hydrologic and ecological analyses. We produce a single file for all monthly values of each variable for individual GCM/emission scenario combination gridded at the given GCMs native resolution. Produced alongside all of the files are descriptions of each of the variables and generated python scripts that contain the functions used to estimate vapor pressure deficit, potential evapotranspiration, and reference evapotranspiration.

FIG. 1 in Ericaria giacconei sp. nov. (Sargassaceae, Fucophyceae), the species to which the invalidly published Cystoseira hyblaea Giaccone should be referred

FIG. 1. — Distribution of Ericaria giacconei sp. nov. white circles indicate stations in which the species was previously recorded as Cystoseira hyblaea Giaccone. The white triangle shows the type locality.

FIG. 5 in Ericaria giacconei sp. nov. (Sargassaceae, Fucophyceae), the species to which the invalidly published Cystoseira hyblaea Giaccone should be referred

FIG. 5. — Ericaria giacconei sp. nov. and Sabellaria alveolata (Linnaeus, 1767) from "Porto Palo di Capo Passero" (Sicily): A, overview of the bottom covered by a E. giacconei and S. alveolata biocostructions; B, A thallus of E. giacconei encircled by S. alveolata.

FIG. 3 in Ericaria giacconei sp. nov. (Sargassaceae, Fucophyceae), the species to which the invalidly published Cystoseira hyblaea Giaccone should be referred

FIG. 3. — Ericaria giacconei sp. nov., holotype: CAT 2716, 11.I.2020, Contrada Guardiana (36°39'03"N, 15°04'37"E), Porto Palo di Capo Passero (Straits of Sicily, Italy), 0.50 m depth: A, habit; B, detail of basal crust; C, detail of apex of cauloid. Scale bars: A, 2 cm; B, C, 1 cm.

FIG. 4 in Ericaria giacconei sp. nov. (Sargassaceae, Fucophyceae), the species to which the invalidly published Cystoseira hyblaea Giaccone should be referred

FIG. 4. — Ericaria giacconei sp. nov., holotype: CAT 2716: A, cross section showing a medulla formed by small rounded cells, a cortex made of roundish cells with thin walls and a meristoderm formed by a layer of rectangular cells twice longer than wide; B, mature receptacles terminal, with deciduous spinous appendages, conceptacles located at the base of spinous deciduous appendages; C, cross section showing a conceptacle with oogonia occupying the floor of the conceptacle and antheridia forming a ring above them; D, detail of antheridia on branched hairs. Scale bars: A, D, 50 µm; B, 0.5 cm; C, 100 µm.

FIG. 2 in Ericaria giacconei sp. nov. (Sargassaceae, Fucophyceae), the species to which the invalidly published Cystoseira hyblaea Giaccone should be referred

FIG. 2. — Ericaria giacconei sp. nov.: Giaccone's specimen labelled as Cystoseira hyblaea Giaccone (CAT 74, preserved in glycerine) showing primary branches with a cupressoid outline. Scale bar: 2 cm.

opencc-by-4.0May 2023View details →

Natural grasslands across mainland France: a dataset including a 10 m raster and ground reference points

The data provided here include the first 10 m raster of natural grasslands across mainland France and related ground reference points. The latter consist of 1,770 field observations that describe natural and artificial grasslands from respectively a compilation of hundreds of field-based vegetation maps and the European Union Land Parcel Identification System (LPIS). The raster data of natural grasslands were derived from five annual 10 m land cover maps of France from 2016-2020. More details can be found on the following reference : Panhelleux, L., Rapinel, S., Hubert-Moy, L., 2023. Natural grasslands across mainland France: a dataset including a 10 m raster and ground reference points. Data in Brief 109348. https://doi.org/10.1016/j.dib.2023.109348

opencc-by-4.0Aug 2003View details →

Fig. 1 in A revised comprehensive checklist, relational database, and taxonomic system of reference for the bristly millipedes of the world (Diplopoda, Polyxenida)

Fig. 1. Polyxenus lagurus (Linnaeus, 1758). Habitus of an adult male, bisexual form, dorsal view, after Nguyen Duy - Jacquemin, 1996 (by kind permission of Millepattia). Drawing by Maurice Gaillard. Length = 4 mm.

opencc-by-4.0Aug 2003View details →

Fig. 2 in A revised comprehensive checklist, relational database, and taxonomic system of reference for the bristly millipedes of the world (Diplopoda, Polyxenida)

Fig. 2. Propolyxenus forsteri Condé, 1951. Habitus of an adult male, dorsal view. Drawing by Christine Beau. Length = 3.5 mm.

dryad40/100

Data from: A global reference database in FAOSTAT of cropland nutrient budgets and nutrient use efficiency: nitrogen, phosphorus and potassium, 1961–2020

Agricultural nutrient budgets help to identify an excess or an insufficiency in use of fertilizers and other nutrient sources. Nutrient budgets allow for indicators such as the nutrient balance (surplus or deficit) and nutrient use efficiency to be estimated. This can help in the monitoring of agricultural productivity and sustainability globally. The present dataset is a global database of country-level budget estimates for nitrogen (N), phosphorus (P) and potassium (K) in cropland. The database is disseminated in FAOSTAT and provides a global reference, synthesizing and continuously updating the state-of-the-art on this topic. The database covers the period 961 to 2020 for 205 countries and territories, as well as regional and global aggregates. Results indicate the wide range in nutrient use and use efficiencies across regions, nutrients, and time. This dataset introduces improvements over previous work in relation to key nutrient coefficients affecting nutrient budgets and use efficiency estimates. This is especially for nutrient removal in crop products, manure nutrient content, atmospheric deposition and crop biological N fixation rates.

opencc-zeroDec 2022View details →

opencc-by-4.0Nov 2023View details →

Haplotype-aware reference genome reveals hidden somatic mutations of sweet orange

Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).   Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).   Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).

opencc-by-4.0May 2023View details →

bksnake_reference_genomes_2022-07-15_hg38

Human hg38 reference genomes and annotations files from RefSeq/NCBI and Ensembl. Archived in a tar.gz file. Files are processed and formatted so that they can be used together with the bulk RNASeq pipeline "bksnake". STAR index files for the genome file are also included. The tar.gz file contains the following data folders <ul> <li>genomes_2022-07-15_hg38/fasta</li> <li>genomes_2022-07-15_hg38/star_2.7.10b</li> <li>genomes_2022-07-15_hg38/gtf/ensembl</li> <li>genomes_2022-07-15_hg38/gtf/refseq</li> </ul> "fasta" contains fasta genomic sequences and index files, as well as ribosomal transcripts "intervals" and chromosome "dictionary" files. "star_2.7.10b" contains STAR aligner index files. "gtf/ensembl" and "gtf/refseq" contain Ensembl and RefSeq gtf files as well as "genePred" and "refFlat" files. The recipe how to generate these files is going to be published in github. The bulk RNASeq pipeline "bksnake" is going to be published in github.