cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100965
title: Supporting data for "Maternal plasma lipids are involved in the pathogenesis of preterm birth"

description: Preterm birth is defined by the onset of labor at a gestational age shorter than 37 weeks and it can lead to premature birth and impose a threat to newborns health. The Puerto Rico PROTECT cohort is a well-characterized prospective birth cohort that was designed to investigate environmental and social contributors to preterm birth in Puerto Rico, where preterm birth rates have been elevated in recent decades. To elucidate possible relationships between metabolites and preterm birth in this cohort, we conducted a nested case-control study to conduct untargeted metabolomic characterization of maternal plasma of 31 preterm birth women and 69 full-term labor controls at 24-28 gestational weeks.<br>A total of 333 metabolites were identified and annotated with liquid chromatography/mass spectrometry. Subsequent weighted gene correlation network analysis shows the fatty acid and carene enriched module has a significant positive association (p-value=8e-04, FDR=0.006) with preterm birth. After controlling for potential clinical confounders, a total of 38 metabolites demonstrated significant changes uniquely associated with preterm birth, where 17 of them were preterm biomarkers. Among seven machine-learning classifiers, the application of random forest achieved the highly accurate and specific prediction (AUC = 0.92) for preterm birth in testing data, demonstrating their strong potential as biomarkers for preterm births. The 17 preterm biomarkers are involved in cell signaling, lipid metabolism, and lipid peroxidation functions. Additional modeling using only the 19 spontaneous preterm births (sPTB) and controls identifies 16 sPTB markers, with an AUC of 0.89 in testing data. Half of the sPTB overlaps with those markers for preterm births. Further causality analysis infers that suberic acid upregulates several fatty acids to promote preterm birth.<br>Altogether, this study demonstrates the involvement of lipids, particularly fatty acids, in the pathogenesis of preterm birth.
DOI: 10.6084/m9.figshare.13850360.v1
title: Illumina RNA-Seq, transcript models

description: Structural annotation/transcript models of RNA (cDNA) sequenced from six different tissues (brain, ileum, lung, ovary, spleen, testis) from the tufted duck on Illumina platform.Raw sequencing data was quality-checked with FastQC, adapters and contamination trimmed with Trimmomatic, quality-checked once again, mapped to the tufted duck reference genome with Hisat2, and transcript models assembled with StringTie2.Trimmomatic options: ${ILLUMINACLIP:TruSeq3-PE_rk.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36}Hisat2 options: ${--dta --rna-strandness RF}Stringtie2 options: ${--fr}
DOI: 10.6084/m9.figshare.13850840.v1
title: PacBio Iso-Seq, transcript models

description: Structural annotation/transcript models of RNA (cDNA) sequenced from six different tissues (brain, ileum, lung, ovary, spleen, testis) from the tufted duck on PacBio platform.Full-length non-chimeric (FLNC) reads were built according to PacBio's IsoSeq3 pipeline (ccs, lima, refine), fasta sequences extracted with Bamtools and poly-A tails trimmed with the TAMA tool tama_flnc_polya_cleanup.py. The FLNC reads were mapped to the tufted duck reference genome with Minimap2 and redundant transcript models collapsed with the TAMA tool tama_collapse.py.ccs options: ${--noPolish --minLength=300 --minPasses=1 --minZScore=-999 --maxDropFraction=0.8 --minPredictedAccuracy=0.8 --minSnr=4}lima options: ${--isoseq --dump-clips --no-pbi -j 4 Teloprime.fasta}refine options: ${Teloprime.fasta}Minimap2 options: ${--secondary=no -a -x splice -u f -C 5}tama_collapse.py options: ${-c 95 -x capped -a 100 -z 100}
DOI: 10.6084/m9.figshare.13851581.v1
title: Functional annotation, Illumina and PacBio transcript models

description: Functional annotation of merged structural annotations from short-read and long-read pipelines and six tissues.Structural annotations (transcript models) were merged with the TAMA tool tama_merge.py, fasta sequences extracted with Bedtools, protein-coding potential inferred with CPC2, open reading frames (ORFs) predicted and translated into amino acid sequences with the TAMA tool tama_orf_seeker.py, putative protein-coding sequences identified in the UniProt/UniRef50 database using blastp, results filtered and final annotation built with the TAMA tools tama_orf_blastp_parser.py and tama_cds_regions_bed_add.py, respectively.tama_merge.py options: ${-a 100 -z 100 -d merge_dup -f filelist.txt}filelist.txt settings, short-reads: "no_cap 2,1,2"filelist.txt settings, long-reads: "capped 1,2,1"bedtools options: ${getfasta -name -split -s}blastp options: ${-evalue 1e-10}<br>
DOI: 10.6084/m9.figshare.13852802.v1
title: Expression atlas

description: The merged dataset of the short-read and long-read structural annotations of six tissues was filtered for UniRef50 hits and an expression atlas created based on support of pipeline/tissue.The TAMA tool tama_mergy.py creates a gene report containing each features's source (pipeline, tissue). This gene report was parsed with tama_merge_report_parser.pl, filtered for UniRef50 hits and loaded in the R function UpSetR to visualise tissue-specific evidence for expressed genes.Parse gene report, prepare for UpSetR: ${tama_merge_report_parser.pl supermerge_hisat2_stringtie_and_thresholds_ends_gene_report.txt gene_report.csv}Get genes with UniRef50 hits in final annotation: ${awk 'BEGIN {FS="[\t;]"} $6 ~ /UniRef50/ {print $4}' supermerge_hisat2_stringtie_and_thresholds_ends.bed | sed 's/$/,/' | sort -u &gt; gene_support_uniprot.txt}Filter UpSetR list for UniRef50-supported entries: ${grep -Ff gene_support_uniprot.txt gene_report.csv &gt; gene_report_supported_by_uniprot.csv}<br>
DOI: 10.6084/m9.figshare.13853756.v1
title: Additional scripts

description: Additional Perl scripts for the tufted duck annotation project and R scripts for visualisation of results.<br>Perl scripts:tama_merge_report_parser.pl: parse gene report of tama_merge.pytblout2gff3.pl: convert cmscan's toblout result to gff3 format<br>R scripts:ncRNA_distributions.R: exons per transcript and transcript length distributionsprotein_coding_potential.R: Venn diagram for CPC2-predicted and UniRef50 identified ORFstranscript_model_histograms.R: histograms for structural annotations per tissue and pipelineUpSetR_uniprot_supported.R: evidence for expressed genes per tissue/pipeline<br>Input files:all_counts_hisat_stringtie_threshold_ends.txt: count data for transcript_model_histograms.Rexons_per_transcripts.txt and transcript_lengths.txt: count data for ncRNA_distributions.Rgene_report_supported_by_uniprot.csv: binary TRUE or FALSE for gene report by tissue/pipeline; input for UpSetR_uniprot_supported.Rgenes_found_cpc.txt and genes_found_uniprot.txt: identified genes CPC2 and UniRef50; input for protein_coding_potential.R
DOI: 10.5281/zenodo.4159414
title: Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data - Table S03 - All detected SVs.xlsx

description: Large concatenated results table on all samples of the Dr. Disco study.
DOI: 10.5524/100939
title: Supporting data for "Fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data"

description: Fusion genes are typically identified by RNA-seq without elucidating the causal genomic breakpoints. However, non poly(A)-enriched RNA-seq contains large proportions of intronic reads spanning also genomic breakpoints. <br>We have developed an algorithm, Dr. Disco, that searches for fusion transcripts without being restricted to splice junctions or annotated exon or genes. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)+ and rRNA-minus RNA-seq data. Comparison with WGS data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG positive tumors were present at RNA level. This revealed tumors in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and mRNA that incorporated intergenic cryptic exons. In breast cancer and glioma samples we identified rearrangement hotspots near CCND1 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. <br>By using the full potential of non poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects.
DOI: 10.5524/100955
title: Supporting data for "<i>Qiber3D</i> - an open-source software package for the quantitative analysis of networks from 3D image stacks"

description: Optical slice microscopy is commonly used to observe cellular morphology in 3D tissue culture, for example, the formation of cell-derived networks. The morphometric quantification of these networks is essential to study the cellular phenotype. Commonly, the quantitative measurements are performed on 2D projections of the image stack resulting in the loss of information in the third dimension. Currently, available 3D image analysis tools rely on manual interactions with the software and are therefore not feasible for large datasets.<br>Here we present <i>Qiber3D</i>, an open-source image processing toolkit. The software package includes the essential image analysis procedures required for image processing, from the raw image to the quantified data. Optional pre-processing steps can be switched on/off depending on the input data to allow for analyzing networks from a variety of sources. Two reconstruction algorithms are offered to meet the requirements for a wide range of network types. Furthermore, <i>Qiber3D</i>s rendering capabilities enable the user to inspect each step of the image analysis process interactively to ensure the creation of an optimal workflow for each application.<br><i>Qiber3D</i> is implemented as a Python package and its source code is freely available at https://github.com/theia-dev/Qiber3D. The toolkit was designed using a building block principle to enable the analysis of a variety of structures, such as vascular networks, neuronal structures, or scaffolds from numerous input formats. While <i>Qiber3D</i> can be used interactively in the Python console, it is aimed at unsupervised automation to process large image datasets efficiently.
DOI: 10.15468/dl.mn77jm
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is SIO Benthic Invertebrate Collection",
 "Country is Croatia"
 ]
}

 The dataset includes 47 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002012-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5524/100952
title: Supporting data for "A Highly Contiguous, Scaffold-level Nuclear Genome Assembly for the Fever Tree (<i>Cinchona pubescens</i> Vahl) as a Novel Resource for Rubiaceae Research"

description: The Andean fever tree (<i>Cinchona</i>L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids which have been key to treating malaria for centuries. In particular, <i>C. pubescens</i> Vahl has been an important source of income for several countries in its native range in north-western South America. However, the genomic resources required to place <i>Cinchona</i> species in the tree of life and to explore the evolution and biosynthesis of alkaloids are meagre. <br>Using a combination of ~120 Gb of long sequencing reads derived from the Oxford Nanopore PromethION platform and 142 Gb of short read Illumina data, we address this gap by providing the first highly contiguous nuclear and organelle genome assemblies and their corresponding annotations. Our nuclear genome assembly consists of 603 scaffolds comprising a total length of 903 Mb, representing ~85% of the genome size (1.1 Gb/1C). This draft genome sequence was complemented by annotating 72,305 CDSs using a combination of <i>de novo</i> and reference-based transcriptome assemblies. Completeness analysis revealed that our assembly is highly complete, displaying 83% of the BUSCO gene set, and a small fraction of genes (4.6%) classified as fragmented. We demonstrate the utility of these novel genomic resources by placing <i>C. pubescens</i> in the Gentianales order using plastid and nuclear datasets. <br>Our study provides the first genomic resource for <i>C. pubescens</i> thus opening new research avenues, including the unravelling of the gene toolkit for alkaloid biosynthesis in the fever tree.
DOI: 10.5524/100887
title: Supporting data for "X-ray micro-tomographic data of live larvae of the beetle <i>Cacosceles newmannii</i>"

description: Quantifying insect respiratory structures and their variation has remained challenging due to their microscopic size. Here we measure insect tracheal volume using X-ray micro-tomography (CT) scanning (at 15 m resolution) on living, sedated larvae of the cerambycid beetle <i>Cacosceles newmannii</i> across a range of body sizes. In this paper we provide the full volumetric data and 3D models for 12 scans, providing novel data on repeatability of imaging analyses and structural tracheal trait differences provided by different image segmentation methods. The volume data is provided here with segmented tracheal regions as 3D models.
DOI: 10.5524/100890
title: Supporting data for "A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen"

description: We report on the largest shotgun metagenomic analysis of the pig gut lumen microbiome to date. By processing over 800 faecal time-series samples from 126 piglets and 42 sows, we generated over 8Tbp of metagenomic shotgun sequence data. This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. In the associated manuscript we describe the animal trial procedures and the generation of our metagenomic dataset. The dataset includes 911 samples, comprising a total of 27 billion raw sequence reads. Preliminary analysis of the dataset consisted in the extraction of 16S rRNA gene containing reads with SortMeRNA and their classification with the RDP classifier.
DOI: 10.5524/100911
title: Supporting data for "ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture"

description: Deep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system which combines 3D printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium.<br><br>We developed a novel deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals.<br><br>Altogether, our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies as well as the screening of clock-related mutants, revealing novel root traits.
DOI: 10.5524/100915
title: Supporting data for "Improved chromosome level genome assembly of the Glanville fritillary butterfly (<i>Melitaea cinxia</i>) based on SMRT Sequencing and linkage map."

description: The Glanville fritillary (<i>Melitaea cinxia</i>) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome level assembly of the butterflys genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with Benchmarking Universal Single-Copy Orthologs (BUSCO) indicates that the genome contains 93 - 95% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome and genetics studies on this species.
DOI: 10.5524/100873
title: Supporting data for "Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis"

description: <i>Rickettsia</i> are intracellular bacteria best known as the causative agents of human and animal diseases. Although these medically important <i>Rickettsia</i> are often transmitted via haematophagous arthropods, other <i>Rickettsia</i>, such as those in the Torix group, appear to reside exclusively in invertebrates and protists with no secondary vertebrate host. Importantly, little is known about the diversity or host range of Torix group <i>Rickettsia</i>.<br>This study describes the serendipitous discovery of <i>Rickettsia</i> amplicons in the Barcode of Life Data System (BOLD), a sequence database specifically designed for the curation of mtDNA barcodes. Out of 184,585 barcode sequences analysed, <i>Rickettsia</i> is observed in approximately 0.41% of barcode submissions and is more likely to be found than <i>Wolbachia</i> (0.17%). The Torix group of <i>Rickettsia</i> are shown to account for 95% of all unintended amplifications from the genus. A further targeted PCR screen of 1,612 individuals from 169 terrestrial and aquatic invertebrate species identified mostly Torix strains and supports the aquatic hot spot hypothesis for Torix infection. Furthermore, the analysis of 1,341 Sequence Read Archive (SRA) deposits indicates Torix infections represent a significant proportion of all <i>Rickettsia</i> symbioses found in arthropod genome projects.<br>This study supports a previous hypothesis which suggests Torix <i>Rickettsia</i> are overrepresented in aquatic insects. In addition, multiple methods reveal further putative hot spots of Torix <i>Rickettsia</i> infection; including in phloem-feeding bugs, parasitoid wasps, spiders, and vectors of disease. The unknown host effects and transmission strategies of these endosymbionts make these newly discovered associations important to inform future directions of investigation involving the understudied Torix <i>Rickettsia</i>.
DOI: 10.5524/100907
title: Supporting data for "ISA API: An open platform for interoperable life science experimental metadata"

description: The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open-source community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab - a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, a JSON serialization ISA-JSON was developed. <br>In this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters and its growing user community. <br>The ISA API provides users with rich programmatic metadata handling functionality to support automation, a common interface and an interoperable medium between the two ISA formats, as well as with other life science data formats required for depositing data in public databases.
DOI: 10.5524/100913
title: Supporting data for "A chromosome-level genome assembly for the Eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology"

description: High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus <i>Sceloporus</i> have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources.<br> We present a high-quality chromosome-level reference genome assembly, SceUnd1.0, (utilizing 10X Genomics Chromium, HiC, and PacBio data) and tissue/developmental stage transcriptomes for the Eastern Fence Lizard, <i>Sceloporus undulatus</i> . We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional <i>Sceloporus</i> species. Finally, we used RNAseq and whole-genome resequencing data to compare three assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium; HiRise Assembly that added data from HiC; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and SNP calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length.<br>These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.