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Figure 2 in R. K. GREVILLE'S FUNGUS NAMED "ORANGE SCLEROTIUM" IS SHOWN TO BE A MEMBER OF THE BOLETALES (FUNGI: BASIDIOMYCOTINA)
Figure 2. Sequence data for type material of Penttilamyces ginnsii compared with those for P. lichenicola and species previously placed in Leucogyrophana.
Figure 1. A, Colour illustration from R. K in R. K. GREVILLE'S FUNGUS NAMED "ORANGE SCLEROTIUM" IS SHOWN TO BE A MEMBER OF THE BOLETALES (FUNGI: BASIDIOMYCOTINA)
Figure 1. A, Colour illustration from R. K. Greville's Scottish Cryptogamic Flora (1824a), Plate 101; B, a specimen of Henderson 9540 (E); C, a specimen of P. D. Orton s.n. (E). Scale bar for B and C: 10 mm. Photographs: R. Watling.
Dataset: Orange County Bancorp, Inc. (OBT) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
The unpatterned orange morph of Philippine Boiga cynodon photographed in 2016 in the University of the Philipines at Los Baños Quezon Land Grant Forest Reserve, Municipality of Siniloan, Quezon Province, southeastern Luzon Island, Photo: Rafe M. Brown. in Synopsis of the Snakes of the Philippines A Synthesis of Data from Biodiversity Repositories, Field Studies, and the Literature
The unpatterned orange morph of Philippine Boiga cynodon photographed in 2016 in the University of the Philipines at Los Baños Quezon Land Grant Forest Reserve, Municipality of Siniloan, Quezon Province, southeastern Luzon Island, Photo: Rafe M. Brown.
Fig. 1 in Oviposition of Anastrepha fraterculus and Ceratitis capitata (Diptera: Tephritidae) in citrus fruits, and development in relation to maturity of orange fruits
Fig. 1. Frequency of oviposition by females of Anastrepha fraterculus (A) and Ceratitis capitata (B) when provided with oranges as an oviposition substrate.
Figure 2 in Lower reproductive rates of Asian citrus psyllid (Hemiptera: Psyllidae) on 'Tahiti' acid lime than on 'Valencia' sweet orange
Figure 2 Frequency (%) of settling of adult Diaphorina citri on V2 shoots of 'Valencia' Sweet orange and 'Tahiti' acid lime plants inside a controlled environment chamber (or room?) (n=10; p= 0.092ns) and in a greenhouse (n=15; p= 0.28ns).
Figure 1 in Lower reproductive rates of Asian citrus psyllid (Hemiptera: Psyllidae) on 'Tahiti' acid lime than on 'Valencia' sweet orange
Figure 1 General schematic representation of set-up process of the different shoot stages of the 2-year-old potted plans of 'Valencia' sweet orange and 'Tahiti' acid lime cv. 'Quebra-Galho', both grafted on 'Cravo' Rangpur lime rootstock, for Diaphorina citri oviposition capacity and nymph survival experiments.
Figure 4 in Lower reproductive rates of Asian citrus psyllid (Hemiptera: Psyllidae) on 'Tahiti' acid lime than on 'Valencia' sweet orange
Figure 4 Mean (±SEM) nymphal duration (duration of development of nymphs from first nymphal stage to adults eclosion) (A/B), nymph viability (percentage of survival of nymphs to adult eclosion) (C/D) and male: female proportion (E/F) ofDiaphorina citri rearing on V3 shoots of 'Valencia' sweet orange and 'Tahiti' acid lime plants under greenhouse conditions. Bars with different letters differ by t test, p<0.05. First repetition n=20; Second repetition n=10.
Figure 5 in Lower reproductive rates of Asian citrus psyllid (Hemiptera: Psyllidae) on 'Tahiti' acid lime than on 'Valencia' sweet orange
Figure 5 Cumulative frequency of adult eclosion of Diaphorina citri on V3 shoots of 'Valencia' sweet orange and 'Tahiti' acid lime under greenhouse conditions. (A) First repetition (n=20); (B) Second repetition (n=10).
Figure 11 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 11. The efficacy of RM of orange peels against human pathogenic bacteria. ****Extremely significant among compared groups at p <0.05 level. Test 1: RM of Valen-cia orange; Test 2: RM of Mandarin orange; Test 3: RM of African navel orange.
Figure 6 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 6. The structure of bioactive compounds of RM of African Navel orange peel (1) Limonene; (2) Hexadecanoic acid, 2-hydroxy-1- (hydroxymethyl) ethyl; (3) 9,12-Octadecadienoic acid (Z,Z)-, methyl ester; (4) Terephthalic acid, di(2-ethylhexyl) ester; (5) α-Sitosterol; (6) α-D-Glucopyranose, 4-O-α-D-galactopyranosyl-; (7) 2-Methoxy-4-vinylphenol; (8) Eugenol; (9) cis-Vaccenic acid; (10) De-canal; (11) Vitamin E; (12) Dichloroxylenol.
Figure 3 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 3. GC-MS chromatogram of the RMs of orange peels. (A) RM of Valencia orange; (B) RM of Mandarin orange; (C) RM of African Navel orange.
Figure 2 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 2. The morphology of orange fruits. (A) Valenica orange; (B) Madarin orange; (C) African Navel orange.
Figure 5 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 5. The structure of bioactive compounds of RM of Mandarin orange peel (1) Lim-onene; (2) Octadecanoic acid, 2-hydroxy-1- (hydroxymethyl) ethyl; (3) Hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl; (4) Tetradecanamide; (5) n-Hexadecanoic acid; (6) α-D-Mannofuranoside, 1-O-(10-undecenyl)-; (7) 3-Deoxy-d-mannoic lactone; (8) Desulpho-sinigrin; (9) 2-Methoxy-4-vinylphenol; (10) Decanal; (11) Vitamin E; (12) 1-Monolinoleoylglycerol trimethylsilyl ether.
Figure 4 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study
Figure 4. The structure of bioactive compounds of RM of Valencia orange peel (1) Limonene; (2) 9-Octadecenamide, (Z)-; (3) Hexadecanoic acid, 2- hy-droxy-1-(hydroxymethyl)ethyl; (4) Octadecanoic acid, 2-hydroxy-1-(hydroxymethyl)ethyl; (5) Tetradecanamide; (6) Hexadecanamide; (7) Ethyl iso-allocholate; (8) Ethyl α-d-glucopyranoside; (9) d-Glycero-d-galacto-heptose; (10) α-Sitosterol; (11) Vitamin E; (12) 4H-1-Benzopyran-4-one, 2-(3,4-dimethoxyphenyl)-5,6,7-trimethoxy-.
Linked collectors and determiners for: A re-description of Cyrtodactylus chrysopylos Bauer (Squamata: Gekkonidae) with comments on the adaptive significance of orange coloration in hatchlings and descriptions of two new species from eastern Myanmar (Burma).
Natural history specimen data linked to collectors and determiners held within, "A re-description of Cyrtodactylus chrysopylos Bauer (Squamata: Gekkonidae) with comments on the adaptive significance of orange coloration in hatchlings and descriptions of two new species from eastern Myanmar (Burma)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d5bea9d0-842b-4959-a3e5-63fcfffb44ae">https://bionomia.net/dataset/d5bea9d0-842b-4959-a3e5-63fcfffb44ae</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d5bea9d0-842b-4959-a3e5-63fcfffb44ae">https://gbif.org/dataset/d5bea9d0-842b-4959-a3e5-63fcfffb44ae</a>. Formatted as a Frictionless Data package.
TYPES: Male holotype from Panama: Panama: Parque Nacional Altos de Campana, 1 hectare PANCODING Inventory, 895 m, 8.68333°, -79.92972°, June 14–19, 2007, M. Arnedo, D. Dimitrov, G. Hormiga, F. Labarque, M. Ramírez, deposited in MIUP, PBI_OON 42313; same data, 1 male paratype deposited in MACN-Ar 29895, PBI_OON 42312. ETYMOLOGY: A noun in apposition; in Greek religion and mythology, Pan is the god of the wild natural world, of shepherds, flocks, and mountains, and of hunting and rustic music. He has hindquarters, legs, and horns of a goat, and the name is here employed to note the large mac- rosetae at the eye region of males that resemble the horns in some illustrations of this god. DIAGNOSIS: This is one of the most autapomor- phic species from the Americas; males have the labium fused with the sternum (fig. 34B), small chelicerae, shorter than the endite length, with anterior blunt projections, and directed backward in lateral view (fig. 34D, E); clypeus directed back- ward (fig. 34D); two light areas on the sternum just below the endites (fig. 34B), carapace almost flat in lateral view and two strong macrosetae at the eye region, pointing forward (fig. 34C–E). Other characters of the male palp, such as the presence of two apophyses, also distinguish this species from others (fig. 38D–F). MALE (PBI_OON 42312): Total length 1.00. Habitus as in figure 34A–C. CEPHALOTHO- RAX: Carapace orange, with brown stripe along in Taxonomic Revision Of The Jumping Goblin Spiders Of The Genus Orchestina Simon, 1882, In The Americas (Araneae: Oonopidae)
TYPES: Male holotype from Panama: Panama: Parque Nacional Altos de Campana, 1 hectare PANCODING Inventory, 895 m, 8.68333°, -79.92972°, June 14–19, 2007, M. Arnedo, D. Dimitrov, G. Hormiga, F. Labarque, M. Ramírez, deposited in MIUP, PBI_OON 42313; same data, 1 male paratype deposited in MACN-Ar 29895, PBI_OON 42312. ETYMOLOGY: A noun in apposition; in Greek religion and mythology, Pan is the god of the wild natural world, of shepherds, flocks, and mountains, and of hunting and rustic music. He has hindquarters, legs, and horns of a goat, and the name is here employed to note the large mac- rosetae at the eye region of males that resemble the horns in some illustrations of this god. DIAGNOSIS: This is one of the most autapomor- phic species from the Americas; males have the labium fused with the sternum (fig. 34B), small chelicerae, shorter than the endite length, with anterior blunt projections, and directed backward in lateral view (fig. 34D, E); clypeus directed back- ward (fig. 34D); two light areas on the sternum just below the endites (fig. 34B), carapace almost flat in lateral view and two strong macrosetae at the eye region, pointing forward (fig. 34C–E). Other characters of the male palp, such as the presence of two apophyses, also distinguish this species from others (fig. 38D–F). MALE (PBI_OON 42312): Total length 1.00. Habitus as in figure 34A–C. CEPHALOTHO- RAX: Carapace orange, with brown stripe along
Text-fig. 2. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., a – holotype 4287/6. Lateral female cones marked by orange arrows; main axis bearing lateral cones marked "Ax". Scale bar 1 cm. in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 2. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., a – holotype 4287/6. Lateral female cones marked by orange arrows; main axis bearing lateral cones marked "Ax". Scale bar 1 cm.
Surf zone circulations and orange paths
<p>Spectrums.zip contains two types of files. The .spt file contain the raw data from the BunkerHill buoy outside Sylt. The fourth entry is the relative PSD of the day, and in the main body of the file the coloumns represent: frequency [Hz], PSD [m^2/Hz], Main direction, directional spreading, Skew, Kurt.<br> The .txt files contains the 2D SWAN spectrums used in the paper. For further description look to: https://swanmodel.sourceforge.io/online_doc/swanuse/node50.html.</p> <p> radsAndCircs.txt contain data about the circulations calculated in the surf zone. Each row corresponds to one circulations, and the coloumns correspond to: <br> Number, tide [m], spreadfactor, main direction [degr], x-location [m], y-location [m], <span class="math-tex">\(\sigma [m], \Gamma_{max} [m^2/s]\)</span>. Then 100 radii and then the 100 corresponding circulations. </p> <p>Tracers.zip contain the 6 orange paths described in the paper. They contain lon/lat coordinates for the oranges sampled at 3Hz. </p> <p>BOSZ_outputs contains all the data from all the runs used in the paper. The .bosz files must be opened with the load_BZ_array.py script. Of interest of the paper are the longitudes and latitudes, X.bosz and Y.bosz; averaged U and V velocites, Ubartmp.bosz and Vbartmp.bosz. The files are stored as a MxN array, where each element correspond to the value of the variable on the calcualted grid. <br> The Drifter.txt files contains all the data of the numerical drifters. They are built up as:<br> time, xDrift1, yDrift1, xDrift2, yDrift2, xDrift3, yDrift3, ...</p> <p>For data about the bathymetry we refer to the LKN.SH. </p>
Haplotype-aware reference genome reveals hidden somatic mutations of sweet orange
<p><strong>Filename: </strong>ASE_in_five_fruit_development.txt</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv</p> <p><strong>Description: </strong>The biallelic genes were identified using the Genespace program.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw</p> <p><strong>Description:</strong> The peaks generated from Control chip-seq.</p> <p> </p> <p><strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf</p> <p><strong>Description: </strong>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).</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_CuteSV.vcf</p> <p><strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv</p> <p><strong>Description: </strong>The gene annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip</p> <p><strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv</p> <p><strong>Description:</strong> The gene annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_genome.fa</p> <p><strong>Filename: </strong>ASE_in_five_fruit_development.txt</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv</p> <p><strong>Description: </strong>The biallelic genes were identified using the Genespace program.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw</p> <p><strong>Description:</strong> The peaks generated from Control chip-seq.</p> <p> </p> <p><strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf</p> <p><strong>Description: </strong>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).</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_CuteSV.vcf</p> <p><strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv</p> <p><strong>Description: </strong>The gene annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip</p> <p><strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv</p> <p><strong>Description:</strong> The gene annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf</p> <p><strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A).</p> <p> </p> <p><strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt</p> <p><strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).</p> <p> </p> <p><strong>Filename: </strong>ASE_in_five_fruit_development.txt</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv</p> <p><strong>Description: </strong>The biallelic genes were identified using the Genespace program.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw</p> <p><strong>Description:</strong> The peaks generated from Control chip-seq.</p> <p> </p> <p><strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf</p> <p><strong>Description: </strong>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).</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_CuteSV.vcf</p> <p><strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv</p> <p><strong>Description: </strong>The gene annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip</p> <p><strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv</p> <p><strong>Description:</strong> The gene annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf</p> <p><strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A).</p> <p> </p> <p><strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt</p> <p><strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).</p> <p> </p> <p><strong>Filename: </strong>ASE_in_five_fruit_development.txt</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv</p> <p><strong>Description: </strong>The biallelic genes were identified using the Genespace program.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw</p> <p><strong>Description:</strong> The peaks generated from Control chip-seq.</p> <p> </p> <p><strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf</p> <p><strong>Description: </strong>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).</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_CuteSV.vcf</p> <p><strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv</p> <p><strong>Description: </strong>The gene annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip</p> <p><strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv</p> <p><strong>Description:</strong> The gene annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf</p> <p><strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A).</p> <p> </p> <p><strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt</p> <p><strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).</p> <p><strong>Filename: </strong>ASE_in_five_fruit_development.txt</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv</p> <p><strong>Description: </strong>The biallelic genes were identified using the Genespace program.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw</p> <p><strong>Description: </strong>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.</p> <p> </p> <p><strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw</p> <p><strong>Description:</strong> The peaks generated from Control chip-seq.</p> <p> </p> <p><strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf</p> <p><strong>Description: </strong>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).</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_CuteSV.vcf</p> <p><strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv</p> <p><strong>Description: </strong>The gene annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip</p> <p><strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype A.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv</p> <p><strong>Description:</strong> The gene annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_gene_model.gff3</p> <p><strong>Description:</strong> The gene structure model of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_genome.fa</p> <p><strong>Description:</strong> The genome sequences of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf</p> <p><strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A).</p> <p> </p> <p><strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt</p> <p><strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).</p> <p><strong>Description:</strong> The genome sequences of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3</p> <p><strong>Description:</strong> The TE annotations of haplotype B.</p> <p> </p> <p><strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf</p> <p><strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A).</p> <p> </p> <p><strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt</p> <p><strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).</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.