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Dataset
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update: {"publication_state"=>["version candidate under curator review", "released"], "release_date"=>[nil, Fri, 05 Apr 2024]}
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2024-04-05T21:32:02Z
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Dataset
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update: {"description"=>["The following files include specimen information, DNA sequence data, and additional information on the analyses used to reconstruct the phylogeny of the leafhopper genus Neoaliturus as described in the Methods section of the original paper:\r\n1.\tTaxon_sampling.csv: contains data on the individual specimens from which DNA was extracted, including sample code, taxon name, collection data (locality, date and name of collector) and museum unique identifier.\r\n2.\tAlignments.zip: a ZIP archive containing 432 separate FASTA files representing the aligned nucleotide sequences of individual gene loci used in the analysis.\r\n3.\tConcatenated_Matrix.fa: is a FASTA file containing the concatenated individual gene alignments used for the maximum likelihood analysis in IQ-TREE.\r\n4.\tGenes_and_Loci.rtf: identifies the individual genes and loci used in the analysis. The partition name is the same as the name of the individual alignment file in the zipped Alignments folder.\r\n5.\tPartitions_best_scheme.nex: is a text file in the standard NEXUS format that indicates the names of the individual data partitions and their locations in the concatenated matrix, and also indicates the substitution model for each partition.\r\n6.\tScripts & Description.zip includes 8 custom shell or perl scripts used to assemble the DNA sequence data by perform reciprocal blast searches between the reference sequences and assemblies for each sample, extract the best sequences based on the blast searches, screen the hits for each locus and keep only the best result, and generate the nucleotide sequence dataset for the predicted orthologues (see the file description.txt for details).\r\n7.\tFull_genetic_distances_matrix.csv shows the genetic distances between pairs of samples in the datset (proportion of nucleotides that differ between samples).", "The following files include specimen information, DNA sequence data, and additional information on the analyses used to reconstruct the phylogeny of the leafhopper genus Neoaliturus as described in the Methods section of the original paper:\r\n1.\tTaxon_sampling.csv: contains data on the individual specimens from which DNA was extracted, including sample code, taxon name, collection data (locality, date and name of collector) and museum unique identifier.\r\n2.\tAlignments.zip: a ZIP archive containing 432 separate FASTA files representing the aligned nucleotide sequences of individual gene loci used in the analysis.\r\n3.\tConcatenated_Matrix.fa: is a FASTA file containing the concatenated individual gene alignments used for the maximum likelihood analysis in IQ-TREE.\r\n4.\tGenes_and_Loci.rtf: identifies the individual genes and loci used in the analysis. The partition name is the same as the name of the individual alignment file in the zipped Alignments folder.\r\n5.\tPartitions_best_scheme.nex: is a text file in the standard NEXUS format that indicates the names of the individual data partitions and their locations in the concatenated matrix, and also indicates the substitution model for each partition.\r\n6.\t(New in this version 2) Scripts & Description.zip includes 8 custom shell or perl scripts used to assemble the DNA sequence data by perform reciprocal blast searches between the reference sequences and assemblies for each sample, extract the best sequences based on the blast searches, screen the hits for each locus and keep only the best result, and generate the nucleotide sequence dataset for the predicted orthologues (see the file description.txt for details).\r\n7.\t(New in this version 2) Full_genetic_distances_matrix.csv shows the genetic distances between pairs of samples in the datset (proportion of nucleotides that differ between samples)."], "version_comment"=>["The original files were submitted to IDB before the associated manuscript (submitted for publication) was reviewed. Referees suggested including 2 additional files, i.e., the scripts used in the bioinformatics pipeline and the full matrix of genetic distances among sequenced individuals in the dataset. The previously included files remain unchanged. We could create a separate IDB deposit for the 2 new files or add them as version 2 of the prevvious dataset. Which is the best option?", "Added 2 new files per journal's suggestion: Scripts_and_description.zip and Full_genetic_distances_matrix.csv."]}
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2024-04-04T16:41:15Z
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RelatedMaterial
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update: {"note"=>[nil, ""]}
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2024-04-04T16:38:28Z
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Dataset
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update: {"description"=>["The following files include specimen information, DNA sequence data, and additional information on the analyses used to reconstruct the phylogeny of the leafhopper genus Neoaliturus as described in the Methods section of the original paper:\r\n1.\tTaxon_sampling.csv: contains data on the individual specimens from which DNA was extracted, including sample code, taxon name, collection data (locality, date and name of collector) and museum unique identifier.\r\n2.\tAlignments.zip: a ZIP archive containing 432 separate FASTA files representing the aligned nucleotide sequences of individual gene loci used in the analysis.\r\n3.\tConcatenated_Matrix.fa: is a FASTA file containing the concatenated individual gene alignments used for the maximum likelihood analysis in IQ-TREE.\r\n4.\tGenes_and_Loci.rtf: identifies the individual genes and loci used in the analysis. The partition name is the same as the name of the individual alignment file in the zipped Alignments folder.\r\n5.\tPartitions_best_scheme.nex: is a text file in the standard NEXUS format that indicates the names of the individual data partitions and their locations in the concatenated matrix, and also indicates the substitution model for each partition.", "The following files include specimen information, DNA sequence data, and additional information on the analyses used to reconstruct the phylogeny of the leafhopper genus Neoaliturus as described in the Methods section of the original paper:\r\n1.\tTaxon_sampling.csv: contains data on the individual specimens from which DNA was extracted, including sample code, taxon name, collection data (locality, date and name of collector) and museum unique identifier.\r\n2.\tAlignments.zip: a ZIP archive containing 432 separate FASTA files representing the aligned nucleotide sequences of individual gene loci used in the analysis.\r\n3.\tConcatenated_Matrix.fa: is a FASTA file containing the concatenated individual gene alignments used for the maximum likelihood analysis in IQ-TREE.\r\n4.\tGenes_and_Loci.rtf: identifies the individual genes and loci used in the analysis. The partition name is the same as the name of the individual alignment file in the zipped Alignments folder.\r\n5.\tPartitions_best_scheme.nex: is a text file in the standard NEXUS format that indicates the names of the individual data partitions and their locations in the concatenated matrix, and also indicates the substitution model for each partition.\r\n6.\tScripts & Description.zip includes 8 custom shell or perl scripts used to assemble the DNA sequence data by perform reciprocal blast searches between the reference sequences and assemblies for each sample, extract the best sequences based on the blast searches, screen the hits for each locus and keep only the best result, and generate the nucleotide sequence dataset for the predicted orthologues (see the file description.txt for details).\r\n7.\tFull_genetic_distances_matrix.csv shows the genetic distances between pairs of samples in the datset (proportion of nucleotides that differ between samples)."]}
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2024-04-04T14:18:53Z
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Dataset
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update: {"hold_state"=>["version candidate under curator review", "none"]}
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2024-04-04T14:11:40Z
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Dataset
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update: {"version_comment"=>[nil, "The original files were submitted to IDB before the associated manuscript (submitted for publication) was reviewed. Referees suggested including 2 additional files, i.e., the scripts used in the bioinformatics pipeline and the full matrix of genetic distances among sequenced individuals in the dataset. The previously included files remain unchanged. We could create a separate IDB deposit for the 2 new files or add them as version 2 of the prevvious dataset. Which is the best option?"]}
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2024-04-03T22:17:44Z
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RelatedMaterial
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create: {"material_type"=>"Dataset", "availability"=>nil, "link"=>"https://doi.org/10.13012/B2IDB-8336414_V1", "uri"=>"10.13012/B2IDB-8336414_V1", "uri_type"=>"DOI", "citation"=>"Sinaiko, Guy; Cao, Yanghui; Dietrich, Christopher H. (2024): Datasets for phylogenomics of the leafhopper genus Neoaliturus Distant. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8336414_V1", "dataset_id"=>2675, "selected_type"=>"Dataset", "datacite_list"=>"IsNewVersionOf", "note"=>nil, "feature"=>nil}
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2024-04-03T22:14:57Z
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RelatedMaterial
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create: {"material_type"=>"Article", "availability"=>nil, "link"=>"", "uri"=>"", "uri_type"=>"", "citation"=>"Sinaiko, G., Cao, Y., & Dietrich, C. H. (in review). Phylogenomics of the leafhopper genus Neoaliturus Distant, 1918 (Hemiptera: Cicadellidae: Deltocephalinae) reveals genetically divergent lineages in the invasive beet leafhopper. Submitted to Molecular Phylogenetics and Evolution ", "dataset_id"=>2675, "selected_type"=>"Article", "datacite_list"=>"", "note"=>"", "feature"=>false}
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2024-04-03T22:14:57Z
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Funder
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create: {"name"=>"U.S. National Science Foundation (NSF)", "identifier"=>"10.13039/100000001", "identifier_scheme"=>"DOI", "grant"=>"DEB-1639601", "dataset_id"=>2675, "code"=>"NSF"}
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2024-04-03T22:14:57Z
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Creator
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create: {"family_name"=>"Dietrich", "given_name"=>"Christopher H.", "identifier"=>"0000-0003-4005-4305", "email"=>"chdietri@illinois.edu", "is_contact"=>true, "row_position"=>3}
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2024-04-03T22:14:57Z
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Dataset
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update: {"corresponding_creator_name"=>[nil, "Christopher H. Dietrich"], "corresponding_creator_email"=>[nil, "chdietri@illinois.edu"], "nested_updated_at"=>[Wed, 03 Apr 2024 22:14:57.557647000 UTC +00:00, Wed, 03 Apr 2024 22:14:57.658062000 UTC +00:00]}
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2024-04-03T22:14:57Z
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Creator
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create: {"family_name"=>"Cao", "given_name"=>"Yanghui", "identifier"=>"0000-0002-0515-0767", "email"=>"caoyh@nwafu.edu.cn", "is_contact"=>false, "row_position"=>2}
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2024-04-03T22:14:57Z
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Creator
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create: {"family_name"=>"Sinaiko", "given_name"=>"Guy", "identifier"=>"0000-0002-3047-7526", "email"=>"guysinaiko@gmail.com", "is_contact"=>false, "row_position"=>1}
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2024-04-03T22:14:57Z
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