cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100135
title: Supporting material for "Reconstructing a comprehensive transcriptome assembly of a white-pupal translocated strain of2 the pest fruit fly Bactrocera cucurbitae."

description: <em>Bactrocera cucurbitae</em> is an important agricultural pest. Basic genomic information is lacking for this species, which could be used to inform methods of control, damage mitigation, and eradication efforts of this pest. A comprehensive transcriptome has been sequenced, assembled, and annotated from a mass-rearing sexing strain of this species. This is a foundational resource that can be leveraged to better understand the physiology and biochemistry of this insect as well as utilized in population genetics.<br>
A transcriptome assembly was constructed containing 17,654 transcript isoforms derived from 10,425 unique genes. This transcriptome size is similar to reports from other Tephritid species and likely includes about 70-80% of the protein coding genes in the genome. The sequence data is publically available in INSDC archives at NCBI/EBI/DDBJ and here we present the InterProScan, BLAST and other analysis results used to annotate the transcriptome, all is provided as a resource to Tephritid researcher community.
DOI: 10.5524/100137
title: Supporting data and materials for "De Novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences".

description: Common chimpanzees (<em>Pan troglodytes</em>) and bonobos (<em>Pan paniscus</em>) are the species most closely related to humans. For this reason, it is especially important to have complete and accurate chimpanzee nucleotide and protein sequences to understand how humans evolved their unique capabilities. We provide transcriptome data from four untransformed cell types derived from the reference <em>Pan troglodytes</em> Clint, to better annotate the chimpanzee genome and provide empirical validation for proposed gene models of this important species. 
RNA was extracted from primary cells cultured from four tissues: skin, adipose stroma, vascular smooth muscle, and skeletal muscle. These four RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the Sequence Read Archive (SRA). Transcripts were assembled, annotated and deposited in the INSDC Transcriptome Shotgun Assembly (TSA) database.
We have provided a high quality annotation of 44,275 transcripts with full-length coding sequence (CDS). This set represented a total of 10,110 unique genes, thus providing empirical support for their existence. This dataset can be used to improve annoannotation of the Pan troglodytes genome.
DOI: 10.5524/100138
title: Supporting materials for "BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ".

description: Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. The Galaxy web-based platform for data intensive biomedical research (http://usegalaxy.org/) offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit). BioMAJ is a widely used and stable software program that is designed to automate the download and transformation of data from various sources.<br>
To ease the process of giving access to reference data in Galaxy, the BioMAJ2Galaxy module has been developed to enable the gap between BioMAJ and Galaxy to be bridged. With this module, it is now possible to configure BioMAJ to automatically download some reference data, to then convert and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers. A snapshot of the code is archived here, but see the genouest GitHub for the most up-to-date version:
<br>
https://github.com/genouest/biomaj2galaxy
<br>
DOI: 10.5524/100140
title: The colorectal adenoma-carcinoma microbiome.

description: Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gutmicrobe(s), however, have not been surveyed in a comprehensive manner. Here we perform a metagenome-wide association study (MGWAS) on stools from advanced adenoma and carcinoma patients and from healthy subjects, revealing microbial genes, strains and functions enriched in each group. An analysis of potential risk factors indicates that high intake of red meat relative to fruits and vegetables appears to associate with outgrowth of bacteria that might contribute to a more hostile gut environment. These findings suggest that faecal microbiome-based strategies may be useful for early diagnosis and treatment of colorectal adenoma or carcinoma.
DOI: 10.5524/100143
title: Software and supporting material for "SMAP: a streamlined methylation pipelinefor bisulphite sequencing".

description: DNA methylation plays important roles in regulating gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has become prevailing in methylation studies due to its cost-effectiveness and single-base resolution. The rapid accumulation of RRBS data demands ingeniously and practically designed analytical tools.
To streamline the data processing of DNA methylation in multiple RRBS samples, we present a flexible pipeline named SMAP, whose features include: 1) it handles single- and/or paired-end (SE/PE) diverse bisulfite sequencing data with reduced false positive rate in differentially methylated regions; 2) it detects allele-specific methylation events with improved algorithm; 3) it has a build-in pipeline for novel single nucleotide polymorphisms (SNP) detection; 4) it supports user-defined multiple restriction enzymes; 5) it basically conducts a one-step operation in all methylation analyses.
SMAP is a modular pipeline implemented in Perl that calls software components written in C/C++, Perl, R and Java. Required input files for SMAP include BS or RRBS data in FASTQ format and a user-defined configuration file including all settings of the pipeline
DOI: 10.5524/100145
title: Supporting data for the dynamics and stabilization of the Human gut microbiome during the first year of life.

description: Here we performed metagenomic shotgun sequencing on fecal samples from 98 full-term Swedish infants (new born, 4-months and 12-months old) and their mothers; assembled gut microbial genomes and constructed reference gene catalogs from the cohort. We generated 1.52 Tb paired-end reads of high-quality sequences (average 3.99 Gb per sample). A gene catalog was constructed for each time point based on de novo assembly and metagenomic gene prediction; and functionally annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. We also assembled a total of 4,356 microbial genomes (&gt;0.9 MB) de novo; by binning assembled contigs according to abundance variations across samples. These de novo assembled genomes were complemented by 1,147 genomes from the National Center for Biotechnology Information (NCBI) Bacteria/Archaea genome database. All genomes were subsequently clustered into 690 unique metagenomic operational taxonomic units (MetaOTUs) that were equivalent to species-level classifications. Of these, 373 were annotated to species, the remaining 317 represent novel species related to known species. We constructed the metaOTUs profile by mapping reads to our metaOTUs sequences.
DOI: 10.5524/100146
title: Supporting material for "Galaxy-M: A galaxy workflow for processing and analysing direct infusion and liquid chromatography mass spectrometry-based metabolomics data".

description: Metabolomics is increasingly recognised as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields, specifically genomics and transcriptomics. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardisation and reproducibility of computational metabolomics tools must to be improved significantly.<br>Here we present an end-to-end metabolomics analysis pipeline that has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics, all wrapped in the Galaxy workflow system. This data repository provides the software and Galaxy configuration files alongside two small test datasets (1xFT-ICR DIMS, 1xLC-MS). <br>To further aid accessibility, the tools, Galaxy and example data are all provided pre-installed in a virtual machine (Ubuntu 14.04LTS 64bit, in the OVF format) that can be downloaded from this repository. <br>Additionally, source code, executables and installation instructions are available from Github and users are encouraged to check this for the most recent updates and additions.<br><br> *****Please note*****<br> It has been reported that there is a problem with the file "Virtual Machine.zip", so we have removed it from our server. <br> We are currently in discussion with the authors to try to rectify this problem. This notice will be removed when we have a working version of the file available. Sorry for any inconvenience.
DOI: 10.5524/100151
title: Supporting data and materials for "Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant".

description: The production of biogas takes place under anaerobic conditions and involves microbial decomposition of organic matter. Most of the participating microbes still have to be considered as unknown and non-cultivable. Accordingly, metagenome sequencing currently is the method of choice to obtain insights into community composition and the genetic repertoire.<br>Here, we report the first deeply sequenced metagenome and metatranscriptome of a complex biogas-producing microbial community from an agricultural production-scale biogas plant. We assembled the metagenome and reconstructed most genes involved in the methane metabolism, a key pathway involving methanogenesis performed by methanogenic Archaea. This exemplary result indicates sufficient sequencing coverage for most downstream analyses. <br>Sequenced at least one order of magnitude deeper than previous studies, our metagenome data will enable novel insights into community composition and the genetic potential of important community members. Moreover, mapping of transcripts to reconstructed genome sequences will enable the identification of active metabolic pathways in target organisms.
DOI: 10.5524/100097
title: Supporting material for: "Rapid detection of structural variation in a Human genome using nanochannel-based genome mapping technology".

description: The nanochannel-based Genome Mapping technology, commercialized as the Irys Platform, 
automatically images fluorescently labeled DNA molecules in a massively parallel 
nanochannel array. This technology has previously been used to map the 4.7-Mb highly 
variable human MHC region, as well as for de novo assembly of a 2.1-Mb region in the 
highly complex <em>Aegilops tauschii</em> genome, lending great promise for use in complete 
genome sequence analysis. 
<br>Here, we apply this rapid and high-throughput genome mapping 
method to discern genome wide structural variations (SVs) as well as explore complex regions based on the YH 
(first Asian genome) cell line.<br> A structural variant (SV) is generally defined as a region of DNA 1 kb and larger in size that is changed with respect to another sample; examples include inversions, translocations, 
deletions, duplications and insertions. Deletions and duplications are also referred to as copy 
number variants (CNVs). Structural variants (SVs) are less common than single nucleotide polymorphisms (SNPs) or insertions/deletions (InDels) in the population but collectively account for a significant fraction of genetic polymorphism and diseases.<br>Utilizing Genome Mapping, we identified 725 SVs including 
InDels, inversions as well as SVs involved in N-base gap regions that are difficult 
to assess by current methods. The data presented here are the processed <em>.tiff</em> image files together with the interpreted <em>.metrics</em> file for each restriction map. <br>
DOI: 10.5524/100099
title: Supporting material for: Paediatric Leukaemia DNA methylation profiling using MBD enrichment and SOLiD Sequencing on archival bone marrow smears.

description: Acute Lymphoblastic Leukaemia(ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from less than 60% chance of survival to over 85% today. The causal molecular mechanisms remain unclear.
We performed SOLiD sequencing on Methyl-Binding Domain(MBD) enriched fractions of genomic DNA from eight paediatric ALL patients using archived bone marrow smear microscope slides. Primary tumour and remission bone marrow sample was analysed. Four patients relapsed and the relapsed tumour was analysed. Input and MBD-enriched DNA from each sample was sequenced, aligned to the hg19 reference genome and analysed for enrichment peaks using MACS and HOMER. In total, 3.67Gb were sequenced, 2.74Gb were aligned to the reference genome (average 74.66% alignment efficiency). 
Our dataset represents one of the first SOLiD MBD-Seq studies performed on paediatric ALL and is the first to utilise archival bone marrow smears.
DOI: 10.5524/100103
title: Supporting materials for the "De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences".

description: Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque; the common marmoset (<i>Callithrix jacchus</i>), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues (skeletal muscle, bladder, hippocampus, cerebral cortex and cerebellum) including both raw sequences (after filtering low quality reads by BLAST against human RefSeq 57) and assembled transcripts, will aid in the annotation of the newly released marmoset genome assembly. Sequences were deposited in the NCBI Sequence Read Archive (PRJNA203643). Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly database (5 Marmoset transcriptomes).
<br>Here we provide the ISA-tab metadata for the entire experiment include sample metadata and links to archived data. In addition we provide the BLASTx (against RefSeq57) results in tabular format for each of the assembled transcriptomes which provides the evidence for the annotations assigned to each transcript.
DOI: 10.5524/100106
title: Supporting material for: "Free breathingly acquired myocardial perfusion data sets for performance analysis of motion compensation algorithms".

description: Perfusion quantification by using first-pass gadolinium-enhanced myocardial perfusion magnetic resonance imaging (MRI) has proved to be a reliable tool for the diagnosis of coronary artery disease that leads to reduced blood flow to the myocardium. <br> Here we present the free breathing perfusion MRI series of ten patients considered clinically to have a stress perfusion defect. For each patient a rest and a stress study was executed. Manual segmentations of the left ventricle myocardium and the right-left ventricle insertion point are provided for all images in order to make a unified validation of the motion compensation algorithms and the perfusion analysis possible. In addition, all the scripts and the software required to run the experiments are provided alongside with the data, and to enable interested parties to directly run the experiments themselves, the test bed is also provided as a virtual hard disk. <br>All of the tools and plugins included in the virtual machine are under open source licenses, but to view the exact version they are under see the license section in the README document.
DOI: 10.5524/100110
title: Supporting material for: "Shared data for IMRT optimization research: the CORT dataset".

description: Here we provide intensity modulation radiation therapy (IMRT) datasets for a prostate case, a liver case, a head and neck
case, and a standard IMRT phantom. For each, we provide the dose-influence
matrix from a variety of beam/couch angle pairs. The dose-influence matrix is
the main entity needed to perform optimizations: it contains the dose to each
patient voxel from each pencil beam. We also provide the original DICOM
computed tomography (CT) scan as well as the DICOM structure file.
DOI: 10.5524/100114
title: A Catalogue of the Mouse Gut Metagenome

description: To increase the value of mice models studies, we have used HiSeq2000-based whole genome sequencing to establish a catalogue of 2.6 million non-redundant microbial genes derived from 1,130 gigabases of microbial sequences from faecal samples of 184 mice of different strains and from different providers and housing laboratories. More than 99% of the genes are bacterial indicating that the mouse gut microbiota comprises at least 800-900 prevalent bacterial species.This reference gene catalog was annotated to Non-redundant protein sequences (NR) and Kyoto Encyclopedia of Genes and Genomes (KEGG) and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) databases.
DOI: 10.5524/100115
title: Single-cell sequencing data using DOP-PCR, MDA and MALBAC whole genome amplification methods.

description: Single-cell sequencing (SCS) provides many biomedical advances but currently relies on whole-genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). Here we systematically compare the advantages and disadvantages and performance of each method. To systematically evaluate the SCS performance of commonly used WGA methods, we performed single cell WGA using six commercial kits based on DOP-PCR and MDA and then performed whole genome sequencing (WGS) of the successfully amplified DNA. 
A total of 36 single cells were collected in our study, 19 from a lymphoblastoid cell-line (YH cell-line), the rest from a widely-known gastric cancer cell-line, BGC823. Corresponding pooled DNA was extracted as a non-amplified control. BGC823 cell-line was provided by Professor Youyong Lv at Beijing Cancer Hospital. All samples and experimental protocols were approved by the Institutional Review Board of BGI-Shenzhen.
DOI: 10.5524/100128
title: The genome of the Indian gharial (<em>Gavialis gangeticus</em>).

description: The Indian gharial (<em>Gavialis gangeticus</em>), also known as the gavial or the fish-eating crocodile, is a crocodilian of the family Gavialidae, native to the Indian Subcontinent. The global gharial population is estimated at fewer than 235 individuals, which are threatened by loss of riverine habitat, depletion of fish resources and use of fishing nets. <br> 
These data have been produced as part of the Crocodilian Genomes Project. Genomic DNA was isolated using blood from an adult female that died of natural causes in 2010. Briefly, the gharial data consisted of Illumina reads from three libraries ranging from 50 to 170x coverage. These reads were assembled using SOAPdenovo v2.04.
DOI: 10.5524/100139
title: Gene-set of brown planthopper genome

description: The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management.<br>
The N. lugens population sequenced in the present study was originally collected in Hangzhou, China, in 2008 and had been reared on rice seedlings (strain: TN1). One male and one female were isolated and mated to produce F1 progeny. A single pair was then selected for sibling inbreeding for 13 generations. Genomic DNA was extracted from adult females of the F13 generation. We constructed a series of DNA libraries with varying insert sizes (180 bp, 200 bp, 500 bp, 2 kb, 5 kb, 10 kb, 20 kb, and 40 kb) to perform WGS sequencing. All of the above libraries were sequenced on Illumina HiSeq 2000 or GA-II sequencers. After performing filtering steps to remove adapter-contaminated reads, low-quality reads, and duplicate reads, a total of 158.01 Gbp of clean WGS data (131.67X of the genome) with 131.7-fold of genome coverage depth and were combined with 507.94 Gbp of clean fosmid sequence data was obtained. This was assembled using SOAPdenovo and Rabbit, producing a final draft assembly of 1.141Gbp with a scaffold N50 of 356,597 bp. The Nilaparvata lugens genome should highlight potential directions for effective pest control of the planthopper.
DOI: 10.5524/100144
title: Supporting data for "Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment".

description: There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specialists for identification and only evaluate small subsets of biodiversity. Environmental DNA (eDNA) approaches are being promoted as a solution to these limitations, but questions remain unresolved. Here we evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life. We compare these data to traditional biodiversity monitoring tools, including mist-netting and call counts for birds, vegetation surveys, and invertebrate collection with DNA barcoding. Our sampling regime consisted of ten 20 × 20 metre plots, each comprising sixteen 5 × 5 metre sub-plots along a 700 metre elevational gradient on a temperate island forest ecosystem.<br>Across five molecular markers (16S, 18S, ITS, COI and trnL) we collected 3,537,908 sequence reads. From six eDNA data sets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 65 NCBI taxonomy-define phyla or equivalent high-level taxa, ranging from 12 (ITS) to 34 phyla (18S) for a given eDNA marker.
DOI: 10.5524/100098
title: Supporting materials for the "Annotated Features of Domestic Cat-Felis catus Genome".

description: Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases including feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors. 
<br>We report here a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia, Mo., bisulfite sequencing of Boris, a male cat from St. Petersburg, and light 30x sequencing of Sylvester, a European wildcat progenitor of domestication. The annotation includes 21,865 protein coding genes identified by comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements and 3,182 microRNA homologues.