cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2bls0r
title: CCDC 2162994: Experimental Crystal Structure Determination

description: Related Article: Jiawei Lin, Muwei Zhang, Niu Sun, Shihui He, Xusheng Zhang, Zhongnan Guo, Jing Zhao, Quanlin Liu, Wenxia Yuan|2022|J.Mater.Chem.C|10|16773|doi:10.1039/D2TC03481F
description: Related Article: Jiawei Lin|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2blrzp
title: CCDC 2162993: Experimental Crystal Structure Determination

description: Related Article: Jiawei Lin, Muwei Zhang, Niu Sun, Shihui He, Xusheng Zhang, Zhongnan Guo, Jing Zhao, Quanlin Liu, Wenxia Yuan|2022|J.Mater.Chem.C|10|16773|doi:10.1039/D2TC03481F
description: Related Article: Jiawei Lin|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cxrgj
title: CCDC 2202378: Experimental Crystal Structure Determination

description: Related Article: Cihang Yu, Bruno A. Piscelli, Nawaf Al Maharik, David B. Cordes, Alexandra M. Z. Slawin, Rodrigo A. Cormanich, David O'Hagan|2022|Chem.Commun.|58|12855|doi:10.1039/D2CC05058G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.21436560
title: SignalP results for signal peptide sequences and DeepTMHMM results for the transmembrane domain.

description: SignalP results for signal peptide sequences and DeepTMHMM results for the transmembrane domain. output_signalP.gff3 and SignalP_results.txt are the output files of SignalP, and DTU_DeepTMHMM_1.0.15-results.zip is the output file of DeepTMHMM. For details, please refer to the references of the software.
DOI: 10.6084/m9.figshare.21351501
title: Domain and phylogenetic analysis of 105 C-type lectins identified in M.separata, using DoMosaics.

description: Domain and phylogenetic analysis of 105 C-type lectins identified in <em>M.separata</em>, using DoMosaics. CTL_tree_domain.jpg is the CTL tree developed using DoMosaics. C_type_lectin_ID.txt shows the ID of C-type lectin genes in <em>M. separata</em>, and CTL.nwk is a new file for the construction of a phylogenetic tree. The CTL.domtree file is the raw file of the CTL_tree_domain.jpg.
DOI: 10.6084/m9.figshare.21351501.v1
title: Domain and phylogenetic analysis of 105 C-type lectins identified in M.separata, using DoMosaics.

description: Domain and phylogenetic analysis of 105 C-type lectins identified in <em>M.separata</em>, using DoMosaics. CTL_tree_domain.jpg is the CTL tree developed using DoMosaics. C_type_lectin_ID.txt shows the ID of C-type lectin genes in <em>M. separata</em>, and CTL.nwk is a new file for the construction of a phylogenetic tree. The CTL.domtree file is the raw file of the CTL_tree_domain.jpg.
DOI: 10.6084/m9.figshare.21386523
title: BLASTp annotation results of the predicted gene set against the NCBI-nr database and count results of the number of species that annotate M. separata genes.

description: BLASTp annotation results of the predicted gene set against the NCBI-nr database and count results of the number of species that annotate <em>M. separata </em>genes. Input _pep.fasta.summary is the result of annotation of <em>M. separata</em> genes against the BLAST_nr database. results.txt contains counting results for the number of species that annotate <em>M. separata </em>genes.
DOI: 10.6084/m9.figshare.21386523.v1
title: BLASTp annotation results of the predicted gene set against the NCBI-nr database and count results of the number of species that annotate M. separata genes.

description: BLASTp annotation results of the predicted gene set against the NCBI-nr database and count results of the number of species that annotate <em>M. separata </em>genes. Input _pep.fasta.summary is the result of annotation of <em>M. separata</em> genes against the BLAST_nr database. results.txt contains counting results for the number of species that annotate <em>M. separata </em>genes.
DOI: 10.6084/m9.figshare.21215255
title: DDBJ/ENA/GenBank accession IDs and FASTA file IDs of assembled genome sequences.

description: DDBJ/ENA/GenBank accession IDs and FASTA file IDs of assembled genome sequences.
DOI: 10.6084/m9.figshare.21215255.v1
title: DDBJ/ENA/GenBank accession IDs and FASTA file IDs of assembled genome sequences.

description: DDBJ/ENA/GenBank accession IDs and FASTA file IDs of assembled genome sequences.
DOI: 10.6084/m9.figshare.21231500
title: Output files of RepeatMasker.

description: Output files of RepeatMasker. Armyworm_genome_seq_finished.fa.out shows the detailed status of all detected transposable elements (TEs) and their repetitive positions. Armyworm_genome_seq_finished.fa.cat.gz shows the sequence comparison between all TEs and genome sequences. Armyworm_genome_seq_finished.fa.masked.gz is the genome sequence in which repetitive and TE sequences are indicated in lowercase letters. See RepeatMasker for detailed explanation (https://www.repeatmasker.org/).
DOI: 10.6084/m9.figshare.21257625
title: Functional annotations of Mythimna separata genes.

description: Functional annotations of <em>Mythimna separata</em> genes. Using the predicted amino acid sequences of <em>M. separata, </em>its genes were functionally annotated using Fanflow4Insects. The predicted amino acid sequences were compared with the gene set data of <em>Homo sapiens</em>, <em>Mus musculus</em>, <em>Caenorhabditis elegans</em>, <em>Drosophila melanogaster</em>, <em>Bombyx mori</em>, <em>Manduca sexta</em>, <em>Apis mellifera</em>, <em>Tribolium castaneum</em>, and UniProtKB/Swiss-Prot dataset. "pid" and "gene_symbol" indicate hit protein IDs and gene symbols of each dataset, respectively. The protein domains were annotated using Pfam and HMMER. DOI: 10.6084/m9.figshare.21257625.
DOI: 10.6084/m9.figshare.21257625.v1
title: Functional annotations of Mythimna separata genes.

description: Functional annotations of <em>Mythimna separata</em> genes. Using the predicted amino acid sequences of <em>M. separata, </em>its genes were functionally annotated using Fanflow4Insects. The predicted amino acid sequences were compared with the gene set data of <em>Homo sapiens</em>, <em>Mus musculus</em>, <em>Caenorhabditis elegans</em>, <em>Drosophila melanogaster</em>, <em>Bombyx mori</em>, <em>Manduca sexta</em>, <em>Apis mellifera</em>, <em>Tribolium castaneum</em>, and UniProtKB/Swiss-Prot dataset. "pid" and "gene_symbol" indicate hit protein IDs and gene symbols of each dataset, respectively. The protein domains were annotated using Pfam and HMMER. DOI: 10.6084/m9.figshare.21257625.
DOI: 10.6084/m9.figshare.21257601
title: Predicted genes, coding sites and amino acid in M. separata

description: Data related to predicted genes, coding sequences and amino acid sequences in M. separata by Braker2. Gene.gtf contains structural data of predicted genes and transcripts. Gene_cds.fasta and gene_pep.fasta contain predicted coding sequences and amino acid sequences respectively
DOI: 10.6084/m9.figshare.21257601.v1
title: Predicted genes, coding sites and amino acid in M. separata

description: Data related to predicted genes, coding sequences and amino acid sequences in M. separata by Braker2. Gene.gtf contains structural data of predicted genes and transcripts. Gene_cds.fasta and gene_pep.fasta contain predicted coding sequences and amino acid sequences respectively
DOI: 10.6084/m9.figshare.21346908
title: ID list of orthologues of the six AMP genes

description: ID list of orthologs of the six antimicrobial peptide (AMP) genes. Orthologs of the six AMP genes (defensin, cecropin, attacin, gloverin, moricin, and lebocin<em>)</em> in <em>M. separata </em>were searched using the annotation results (DOI: 10.6084/m9.figshare.21257625). The <em>M. separata</em> gene set IDs of the AMP orthologs are listed.
DOI: 10.6084/m9.figshare.21346908.v1
title: ID list of orthologues of the six AMP genes

description: ID list of orthologs of the six antimicrobial peptide (AMP) genes. Orthologs of the six AMP genes (defensin, cecropin, attacin, gloverin, moricin, and lebocin<em>)</em> in <em>M. separata </em>were searched using the annotation results (DOI: 10.6084/m9.figshare.21257625). The <em>M. separata</em> gene set IDs of the AMP orthologs are listed.
DOI: 10.5281/zenodo.7333024
title: Spain fuel prices

description: This dataset provides insight into: All fuel types available at each petrol station Covers all petrol stations of Spain Informs fuel price evolution along wk46, 2022
description: {"references": ["https://geoportalgasolineras.es/geoportal-instalaciones/Inicio", "https://energia.gob.es/en-us/Paginas/index.aspx"]}
DOI: 10.5281/zenodo.7333023
title: Spain fuel prices

description: This dataset provides insight into: All fuel types available at each petrol station Covers all petrol stations of Spain Informs fuel price evolution along wk46, 2022
description: {"references": ["https://geoportalgasolineras.es/geoportal-instalaciones/Inicio", "https://energia.gob.es/en-us/Paginas/index.aspx"]}
DOI: 10.6084/m9.figshare.21325707
title: BLASTx results for genes in the Toll and immune deficiency (IMD) pathways.

description: BLASTx results for genes in the Toll and immune deficiency (IMD) pathways. BLASTx was performed using either <em>Drosophila melanogaster</em> transcript sequences consisting of the Toll (ID: FBgg0001194) or IMD (ID: FBgg0001059) pathway components in Flybase as query sequences and<em> M.</em> <em>separata</em>’s predicted amino acid sequences as subject sequences.
DOI: 10.6084/m9.figshare.21325707.v1
title: BLASTx results for genes in the Toll and immune deficiency (IMD) pathways.

description: BLASTx results for genes in the Toll and immune deficiency (IMD) pathways. BLASTx was performed using either <em>Drosophila melanogaster</em> transcript sequences consisting of the Toll (ID: FBgg0001194) or IMD (ID: FBgg0001059) pathway components in Flybase as query sequences and<em> M.</em> <em>separata</em>’s predicted amino acid sequences as subject sequences.
DOI: 10.6084/m9.figshare.21325740
title: BLASTp results for genes in the Toll and immune deficiency (IMD) pathways.

description: BLASTp results for genes in the Toll and immune deficiency (IMD) pathways. BLASTp was performed using either <em>D. melanogaster</em> amino acid sequences consisting of the Toll (ID: FBgg0001194) or IMD (ID: FBgg0001059) pathway components in Flybase as query sequences and <em>M.</em> <em>separata</em>’s predicted amino acid sequences as subject sequences.
DOI: 10.6084/m9.figshare.21082570
title: Sequence Read Archive accession IDs of raw sequence data in this study.

description: Sequence Read Archive accession IDs of raw sequence data in this study.
DOI: 10.6084/m9.figshare.21082570.v1
title: Sequence Read Archive accession IDs of raw sequence data in this study.

description: Sequence Read Archive accession IDs of raw sequence data in this study.
DOI: 10.6084/m9.figshare.21230882
title: Consensus sequences of transposable elements in M. separata

description: Consensus sequences of transposable elements in M. separata. The consensus sequences of transposable elements in M. separata were constructed by RepeatModeler2. The sequence files are fasta file and stk file from RepeatModeler2.
DOI: 10.6084/m9.figshare.21230882.v1
title: Consensus sequences of transposable elements in M. separata

description: Consensus sequences of transposable elements in M. separata. The consensus sequences of transposable elements in M. separata were constructed by RepeatModeler2. The sequence files are fasta file and stk file from RepeatModeler2.
DOI: 10.6084/m9.figshare.14140875.v1
title: Marker counter-selection via CRISPR/Cas9 co-targeting for efficient generation of genome edited avian cell lines and germ cells

description: Efficient isolation of genetically modified cells that are phenotypically indistinguishable from the unmodified cells remains a major technical barrier for the broader utilization of CRISPR/Cas9. Here, we report a novel enrichment approach to select the genome engineered cells by co-targeting a genomically integrated GFP gene along with the endogenous gene of interest (GOI). Using this co-targeting approach, multiple genomic loci were successfully targeted in chicken (DF1) and quail (CEC-32) fibroblast cell lines by transient transfection of Cas9 and guide RNAs (gRNAs). Clonal isolation of co-targeted DF1 cells showed 75% of cell clones had deletion of GFP and biallelic deletion of the GOI. To assess the utility of this approach to generate genome modified animals, we tested it on chicken primordial germ cells (PGCs) expressing GFP by co-targeting with gRNAs against GFP and endogenous ovomucoid (OVM) gene. PGCs enriched for loss of GFP and confirmed for OVM deletion, derived by co-targeting, were injected into Hamburger and Hamilton stage 14–15 chicken embryos, and their ability to migrate to the genital ridge was confirmed. This simple, efficient enrichment approach could easily be applied to the creation of knock-out or edited cell lines or animals.
DOI: 10.6084/m9.figshare.14140875
title: Marker counter-selection via CRISPR/Cas9 co-targeting for efficient generation of genome edited avian cell lines and germ cells

description: Efficient isolation of genetically modified cells that are phenotypically indistinguishable from the unmodified cells remains a major technical barrier for the broader utilization of CRISPR/Cas9. Here, we report a novel enrichment approach to select the genome engineered cells by co-targeting a genomically integrated GFP gene along with the endogenous gene of interest (GOI). Using this co-targeting approach, multiple genomic loci were successfully targeted in chicken (DF1) and quail (CEC-32) fibroblast cell lines by transient transfection of Cas9 and guide RNAs (gRNAs). Clonal isolation of co-targeted DF1 cells showed 75% of cell clones had deletion of GFP and biallelic deletion of the GOI. To assess the utility of this approach to generate genome modified animals, we tested it on chicken primordial germ cells (PGCs) expressing GFP by co-targeting with gRNAs against GFP and endogenous ovomucoid (OVM) gene. PGCs enriched for loss of GFP and confirmed for OVM deletion, derived by co-targeting, were injected into Hamburger and Hamilton stage 14–15 chicken embryos, and their ability to migrate to the genital ridge was confirmed. This simple, efficient enrichment approach could easily be applied to the creation of knock-out or edited cell lines or animals.
DOI: 10.6084/m9.figshare.14039705.v2
title: Response of the ileum transcriptome to fructo-oligosaccharides in Taiping chickens

description: The aim of this study was to investigate the effects of fructo-oligosaccharide (FOS) supplementation intake of Taiping chickens (<i>Gallus gallus domesticus</i>) and its stimulating effects on ileum. 120 healthy chickens were randomly divided into two groups; control group (CT) and fructo-oligosaccharides group (FOS). At the 60th day of age, ileum mucosa of three chickens per group were collected and performed transcriptome profiling of Taiping chicken ileum mucosa using the Hiseq™ 2500 sequencing platform. Compared with CT group, 50 genes were differentially expressed in the FOS group. Ten of the differently expressed genes were further validated by RT-qPCR. In addition, gene ontology and Kyoto encyclopedia of genes and genomes analyses revealed that these differentially expressed genes were mainly enriched to drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, retinol metabolism, fat digestion and absorption, herpes simplex infection and valine, leucine and isoleucine biosynthesis. The results of this study provided the help to our understanding application of fructo-oligosaccharides in indigenous chicken production and provide a theoretical basis for the genetic development of indigenous chickens.
DOI: 10.6084/m9.figshare.13663654
title: Detection and whole genome sequencing of murine norovirus in animal facility in Italy

description: Viruses belonging to the genus <i>Norovirus</i> (NoV) of the family <i>Caliciviridae</i> are the major cause of acute viral gastroenteritis worldwide. NoVs are classified into 10 genogroups (GI-GX), and those belonging to the genogroup GV are able to infect several species of rodents. To evaluate the circulation of MNV among mice housed in an Italian facility, sampling was performed over two separate periods, in 2011, and 3 years later in 2014. During the two samplings, 75 fecal samples were collected from healthy mice housed in the animal facility and subjected to RT-PCR for viral detection. After the analysis, 41/75 animals (54.6%) resulted positive for the presence of MNV in feces. Nucleotide sequencing revealed the presence of two MNV variants co-circulating in both 2011 and 2014. One MNV strain was isolated on RAW264.7 cell line, and subjected to full genome sequencing. Our study showed that the murine noroviruses are widespread in the investigated animal facility, despite guidelines for animal care and maintenance. Full genome sequence analysis of the MNV strain described in this study showed a correlation with other strains circulating in Europe. Understanding the molecular epidemiology of this virus should give insight into its natural history and evolution in mice.
DOI: 10.6084/m9.figshare.13663654.v1
title: Detection and whole genome sequencing of murine norovirus in animal facility in Italy

description: Viruses belonging to the genus <i>Norovirus</i> (NoV) of the family <i>Caliciviridae</i> are the major cause of acute viral gastroenteritis worldwide. NoVs are classified into 10 genogroups (GI-GX), and those belonging to the genogroup GV are able to infect several species of rodents. To evaluate the circulation of MNV among mice housed in an Italian facility, sampling was performed over two separate periods, in 2011, and 3 years later in 2014. During the two samplings, 75 fecal samples were collected from healthy mice housed in the animal facility and subjected to RT-PCR for viral detection. After the analysis, 41/75 animals (54.6%) resulted positive for the presence of MNV in feces. Nucleotide sequencing revealed the presence of two MNV variants co-circulating in both 2011 and 2014. One MNV strain was isolated on RAW264.7 cell line, and subjected to full genome sequencing. Our study showed that the murine noroviruses are widespread in the investigated animal facility, despite guidelines for animal care and maintenance. Full genome sequence analysis of the MNV strain described in this study showed a correlation with other strains circulating in Europe. Understanding the molecular epidemiology of this virus should give insight into its natural history and evolution in mice.
DOI: 10.6084/m9.figshare.14039705
title: Response of the ileum transcriptome to fructo-oligosaccharides in Taiping chickens

description: The aim of this study was to investigate the effects of fructo-oligosaccharide (FOS) supplementation intake of Taiping chickens (<i>Gallus gallus domesticus</i>) and its stimulating effects on ileum. 120 healthy chickens were randomly divided into two groups; control group (CT) and fructo-oligosaccharides group (FOS). At the 60th day of age, ileum mucosa of three chickens per group were collected and performed transcriptome profiling of Taiping chicken ileum mucosa using the Hiseq™ 2500 sequencing platform. Compared with CT group, 50 genes were differentially expressed in the FOS group. Ten of the differently expressed genes were further validated by RT-qPCR. In addition, gene ontology and Kyoto encyclopedia of genes and genomes analyses revealed that these differentially expressed genes were mainly enriched to drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, retinol metabolism, fat digestion and absorption, herpes simplex infection and valine, leucine and isoleucine biosynthesis. The results of this study provided the help to our understanding application of fructo-oligosaccharides in indigenous chicken production and provide a theoretical basis for the genetic development of indigenous chickens.
DOI: 10.6084/m9.figshare.14068532
title: Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (<i>Bos mutus</i>)

description: Wild yak (<i>Bos mutus</i>) is a vulnerable bovine species on the Qinghai–Tibetan Plateau (QTP). So far, most studies on molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., <i>SRY4</i>, <i>USP9Y</i>, <i>UTY19</i>, <i>AMELY3</i>, <i>OFD1Y10</i> and <i>INRA189</i>), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity (Hd) at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) with four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. This study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.
DOI: 10.6084/m9.figshare.14068532.v2
title: Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (<i>Bos mutus</i>)

description: Wild yak (<i>Bos mutus</i>) is a vulnerable bovine species on the Qinghai–Tibetan Plateau (QTP). So far, most studies on molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., <i>SRY4</i>, <i>USP9Y</i>, <i>UTY19</i>, <i>AMELY3</i>, <i>OFD1Y10</i> and <i>INRA189</i>), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity (Hd) at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) with four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. This study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.