cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20122895.v1
title: Psychometric assessment of the Persian translation of the COVID-19 attitudes and behaviors (ACAB)

description: The data belongs to the study titled: <strong>Psychometric assessment of the Persian translation of the COVID-19 attitudes and behaviors (ACAB)</strong>
DOI: 10.35077/pod
title: 604709

description: This is a series of serial two-photon images of whole mouse brain to characterize cell populations for the purpose of evaluating the specificity of newly created enhancer elements
description: DATASET METADATA: title:'604709', GeneralModality:'population imaging', Technique:'enhancer virus labeling' SPECIMEN METADATA: LocalID:'604709', Species:'Mouse', NCBITaxonomy:'NCBI:txid10090', Age:'54.0', Ageunit:'Days', Sex:'Male', Genotype:'Ai193(TICL-EGFP-ICF-tdT)-hyg/wt', OrganLocalID:'1143409294.0', OrganName:'Brain', SampleLocalID:'0539070438' INSTRUMENT METADATA: MicroscopeType:'Two Photon', MicroscopeManufacturerAndModel:'TissueVision TissueCyte 1000', ObjectiveName:'Zeiss 20X Plan-Apochromat', ObjectiveImmersion:'Water', ObjectiveNA:'1.0', ObjectiveMagnification:'20X', DetectorType:'PMT', DetectorModel:'Hamamatsu R3896', IlluminationWavelength:'925nm', DetectionWavelength:'447-593nm', SampleTemperature:'20.0' IMAGE METADATA: xAxis:'left-to-right', yAxis:'superior-to-inferior', zAxis:'posterior-to-anterior', Number:'1,2,3,red,green,blue', displayColor:'(1.0,0.0,0.0),(0.0,1.0,0.0),(0.0,0.0,1.0)', Representation:'neurite', Flurophore:'CH1(background fluorescence) CH2(GFP) CH3(background fluorescence)', stepSizeX:'0.35', stepSizeY:'0.35', stepSizeZ:'100.0', Channels:'3.0', Slices:'140.0', z:'1.0', Xsize:'40000.0', Ysize:'30000.0', Zsize:'1.0'
DOI: 10.5281/zenodo.6563473
title: AmelHap pilot: filter4 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to exclude samples or variants with call rate &lt;90% in the filter3 dataset, leaving 14.8M variants. A subset of this dataset comprising 1.8M variants is included, in which variants were pruned to remove those in high linkage disequilibrium (r<sup>2</sup> &gt; 0.1 for variant pairs up to 10kb apart). The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.5281/zenodo.6563472
title: AmelHap pilot: filter4 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to exclude samples or variants with call rate &lt;90% in the filter3 dataset, leaving 14.8M variants. A subset of this dataset comprising 1.8M variants is included, in which variants were pruned to remove those in high linkage disequilibrium (r<sup>2</sup> &gt; 0.1 for variant pairs up to 10kb apart). The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.5281/zenodo.6563443
title: AmelHap pilot: filter3 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to monomorphic variants in the filter2 dataset, leaving 16.2M variants. The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.5281/zenodo.6563442
title: AmelHap pilot: filter3 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to monomorphic variants in the filter2 dataset, leaving 16.2M variants. The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.5281/zenodo.6563420
title: AmelHap pilot: filter2 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to mask genotypes with 'FORMAT/DP&gt;100 | FORMAT/GQ&lt;40' in the filter1 dataset, retaining all 16.6M variants. The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.5281/zenodo.6563419
title: AmelHap pilot: filter2 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to mask genotypes with 'FORMAT/DP&gt;100 | FORMAT/GQ&lt;40' in the filter1 dataset, retaining all 16.6M variants. The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.5281/zenodo.6563399
title: AmelHap pilot: filter1 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to exclude variants with 'QD&lt;20 || QD&gt;40 || MQ &lt; 50 || SOR &gt;3' in the raw dataset, leaving 16.6M variants. The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.5281/zenodo.6563398
title: AmelHap pilot: filter1 data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to exclude variants with 'QD&lt;20 || QD&gt;40 || MQ &lt; 50 || SOR &gt;3' in the raw dataset, leaving 16.6M variants. The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.
DOI: 10.35077/pop
title: 604710

description: This is a series of serial two-photon images of whole mouse brain to characterize cell populations for the purpose of evaluating the specificity of newly created enhancer elements
description: DATASET METADATA: title:'604710', GeneralModality:'population imaging', Technique:'enhancer virus labeling' SPECIMEN METADATA: LocalID:'604710', Species:'Mouse', NCBITaxonomy:'NCBI:txid10090', Age:'54.0', Ageunit:'Days', Sex:'Male', Genotype:'Ai193(TICL-EGFP-ICF-tdT)-hyg/wt', OrganLocalID:'1143409539.0', OrganName:'Brain', SampleLocalID:'0539070442' INSTRUMENT METADATA: MicroscopeType:'Two Photon', MicroscopeManufacturerAndModel:'TissueVision TissueCyte 1000', ObjectiveName:'Zeiss 20X Plan-Apochromat', ObjectiveImmersion:'Water', ObjectiveNA:'1.0', ObjectiveMagnification:'20X', DetectorType:'PMT', DetectorModel:'Hamamatsu R3896', IlluminationWavelength:'925nm', DetectionWavelength:'447-593nm', SampleTemperature:'20.0' IMAGE METADATA: xAxis:'left-to-right', yAxis:'superior-to-inferior', zAxis:'posterior-to-anterior', Number:'1,2,3,red,green,blue', displayColor:'(1.0,0.0,0.0),(0.0,1.0,0.0),(0.0,0.0,1.0)', Representation:'neurite', Flurophore:'CH1(background fluorescence) CH2(GFP) CH3(background fluorescence)', stepSizeX:'0.35', stepSizeY:'0.35', stepSizeZ:'100.0', Channels:'3.0', Slices:'140.0', z:'1.0', Xsize:'40000.0', Ysize:'30000.0', Zsize:'1.0'
DOI: 10.5281/zenodo.6685365
title: Experimental Calendar Ageing Data for Lithium-Ion Battery Chemistries

description: This data set has been generated by Technische Hochschule Ingolstadt (THI). If there are any questions,<br> please do not hesitate to get in touch with the authors.
DOI: 10.5281/zenodo.6546753
title: Experimental Calendar Ageing Data for Lithium-Ion Battery Chemistries

description: This data set has been generated by Technische Hochschule Ingolstadt (THI). If there are any questions,<br> please do not hesitate to get in touch with the authors.
DOI: 10.5281/zenodo.6563237
title: AmelHap pilot: raw data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is unfiltered, and contains all variants regardless of quality or call rate.
DOI: 10.5281/zenodo.6563236
title: AmelHap pilot: raw data

description: Honey bee <em>Apis mellifera</em> drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is unfiltered, and contains all variants regardless of quality or call rate.
DOI: 10.35077/pot
title: 604711

description: This is a series of serial two-photon images of whole mouse brain to characterize cell populations for the purpose of evaluating the specificity of newly created enhancer elements
description: DATASET METADATA: title:'604711', GeneralModality:'population imaging', Technique:'enhancer virus labeling' SPECIMEN METADATA: LocalID:'604711', Species:'Mouse', NCBITaxonomy:'NCBI:txid10090', Age:'54.0', Ageunit:'Days', Sex:'Male', Genotype:'Ai193(TICL-EGFP-ICF-tdT)-hyg/wt', OrganLocalID:'1143409619.0', OrganName:'Brain', SampleLocalID:'0539070448' INSTRUMENT METADATA: MicroscopeType:'Two Photon', MicroscopeManufacturerAndModel:'TissueVision TissueCyte 1000', ObjectiveName:'Zeiss 20X Plan-Apochromat', ObjectiveImmersion:'Water', ObjectiveNA:'1.0', ObjectiveMagnification:'20X', DetectorType:'PMT', DetectorModel:'Hamamatsu R3896', IlluminationWavelength:'925nm', DetectionWavelength:'447-593nm', SampleTemperature:'20.0' IMAGE METADATA: xAxis:'left-to-right', yAxis:'superior-to-inferior', zAxis:'posterior-to-anterior', Number:'1,2,3,red,green,blue', displayColor:'(1.0,0.0,0.0),(0.0,1.0,0.0),(0.0,0.0,1.0)', Representation:'neurite', Flurophore:'CH1(background fluorescence) CH2(GFP) CH3(background fluorescence)', stepSizeX:'0.35', stepSizeY:'0.35', stepSizeZ:'100.0', Channels:'3.0', Slices:'140.0', z:'1.0', Xsize:'40000.0', Ysize:'30000.0', Zsize:'1.0'
DOI: 10.5281/zenodo.6685324
title: Halcyon malimbica decontaminated gx

description: .
DOI: 10.5281/zenodo.6685323
title: Halcyon malimbica decontaminated gx

description: .
DOI: 10.35077/pox
title: 609037

description: This is a series of serial two-photon images of whole mouse brain to characterize cell populations for the purpose of evaluating the specificity of newly created enhancer elements
description: DATASET METADATA: title:'609037', GeneralModality:'population imaging', Technique:'enhancer virus labeling' SPECIMEN METADATA: LocalID:'609037', Species:'Mouse', NCBITaxonomy:'NCBI:txid10090', Age:'58.0', Ageunit:'Days', Sex:'Male', Genotype:'wt/wt', OrganLocalID:'1141460382.0', OrganName:'Brain', SampleLocalID:'0539071286' INSTRUMENT METADATA: MicroscopeType:'Two Photon', MicroscopeManufacturerAndModel:'TissueVision TissueCyte 1000', ObjectiveName:'Zeiss 20X Plan-Apochromat', ObjectiveImmersion:'Water', ObjectiveNA:'1.0', ObjectiveMagnification:'20X', DetectorType:'PMT', DetectorModel:'Hamamatsu R3896', IlluminationWavelength:'925nm', DetectionWavelength:'447-593nm', SampleTemperature:'20.0' IMAGE METADATA: xAxis:'left-to-right', yAxis:'superior-to-inferior', zAxis:'posterior-to-anterior', Number:'1,2,3,red,green,blue', displayColor:'(1.0,0.0,0.0),(0.0,1.0,0.0),(0.0,0.0,1.0)', Representation:'neurite', Flurophore:'CH1(background fluorescence) CH2(GFP) CH3(background fluorescence)', stepSizeX:'0.35', stepSizeY:'0.35', stepSizeZ:'100.0', Channels:'3.0', Slices:'140.0', z:'1.0', Xsize:'40000.0', Ysize:'30000.0', Zsize:'1.0'