Find research datasets worth reusing

opencc-by-4.0Aug 2021View details →

Assessing reproduciblity of Inherited Variants Detected with Short-read Whole Genome Sequencing

This dataset is part of the following study: <a href="https://www.fda.gov/science-research/bioinformatics-tools/microarraysequencing-quality-control-maqcseqc">https://www.fda.gov/science-research/bioinformatics-tools/microarraysequencing-quality-control-maqcseqc</a> The raw sequencing data can be downloaded from SRA: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA723125">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA723125</a> and NODE: <a href="https://www.biosino.org/node/project/detail/OEP0018966">https://www.biosino.org/node/project/detail/OEP0018966</a>

opencc-zeroAug 2021View details →

Improving the efficiency of single cell genome sequencing based on overlapping pooling strategy

Single cell genome sequencing has become a useful tool in medicine and biology studies. However, an independent library is required for each cell in single cell genome sequencing, so that the cost grows in step with the number of cells. In this study, we report a study on efficient single-cell copy number variation (CNV) analysis based on overlapping pooling strategy together with branch and bound (B&B) algorithm. Single cells are overlapped pooled before sequencing, and later are assorted into specific types by estimating their CNV patterns by B&B algorithm. Instead of constructing libraries for each cell, a library is required only for each pool. As long as the number of pools is smaller than the cells, fewer libraries are needed, and a lower cost is spent. Through computer simulations, we overlapping pooled 80 cells into 40 and 27 pools and classified them into cell types based on CNV pattern. The results showed that 84% cells in 40 pools and 76.5% cells in 27 pools were correctly classified on average, while only half or one-third of the sequencing libraries are required. Combining with traditional approaches, our method is expected to significantly improve the efficiency of single cell genome sequencing.

opencc-zeroDec 2020View details →

List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)

The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulfite sequencing is commonly used for assessing genome-wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulfite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but there is no independent evaluation of such tools for non-model species, which often lack genomic references. Here, we used whole-genome bisulfite sequencing (WGBS) data from four female great tits (Parus major) to evaluate the performance of seven tools for SNP calling from bisulfite sequencing data. We used SNPs from whole-genome resequencing data of the same samples as baseline SNPs to assess common performance metrics like sensitivity, precision, and the number of true positive, false positive, and false negative SNPs for the full range of variant and genotype quality values. We found clear differences between the tools in either optimizing precision (Bis-SNP), sensitivity (biscuit), or a compromise between both (all other tools). Overall, the choice of SNP caller strongly depends on which performance parameter should be maximized and whether ascertainment bias should be minimized to optimize downstream analysis, highlighting the need for studies that assess such differences.

opencc-by-4.0Oct 2022View details →

Primers for whole genome sequencing of the Sars-Cov-2 virus

Here is the primer sequence for amplification and sequencing of the whole genome of the Sars-Cov-2 virus.

opencc-zeroNov 2022View details →

Efficient Real-Time Selective Genome Sequencing on Resource-Constrained Devices

This dataset contains the curated nanopore raw signal data in <a href="https://www.nature.com/articles/s41587-021-01147-4">BLOW5 format </a>used to benchmark <a href="https://github.com/beebdev/HARU/">Hardware Accelerated Read Until (HARU)</a>. This dataset was created by using the publicly available datasets: <a href="https://community.artic.network/t/links-to-raw-fast5-fastq-data-for-artic-protocol/17">SARS-CoV-2 SP1</a> (1.382M reads) and <a href="https://ncbi.nlm.nih.gov/sra/SRX11368475">NA12878 PromethION subset</a> (500,000 reads). The tarball when extracted will have the following directory structure: haru-data ├── na12878-rfc1 │   ├── blow5-rawsignal │   │   ├── na12878_dna_0.blow5 │   │   ├── na12878_dna_100.blow5 │   │   ├── na12878_dna_101.blow5 │   │   ├── na12878_dna_102.blow5 │   │   ├── ... │   └── reference │       └── rfc1.fa └── SARS-CoV-2-sp1     ├── blow5-rawsignal     │   ├── readgroup0     │   │   ├── reads_0_0.blow5     │   │   ├── reads_0_10.blow5     │   │   ├── reads_0_11.blow5     │   │   ├── reads_0_12.blow5     │   │   ├── ...     │   └── readgroup1     │       ├── reads_1_0.blow5     │       ├── reads_1_10.blow5     │       ├── reads_1_11.blow5     │       ├── ....     └── reference         └── nCoV-2019.reference.fasta nCoV-2019.reference.fasta is the SARS-CoV-2 MN908947.3 reference genome. rfc1.fa is the genomic region hr4:39262456-39391375 extracted from hg38 human genome.

opencc-zeroNov 2022View details →

Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera

Many lepidopteran caterpillars produce silk, cocoons, feeding tubes, or nests for protection from predators and parasites. Yet, the number of lepidopteran species whose silk composition has been studied in detail is very small, because the genes encoding the major structural silk proteins tend to be large and repetitive, making their assembly and sequence analysis difficult. Here we have analyzed the silk of Yponomeuta cagnagella, which represents one of the early diverging lineages of the ditrysian Lepidoptera thus improving the coverage of the order. To obtain a comprehensive list of the Y. cagnagella silk genes, we sequenced, assembled, and annotated the draft genome using Oxford Nanopore and Illumina technologies. The 626 Mb assembly with N50 of 96.5 kb contained 96.9% insect orthologs recovered by BUSCO and 30,003 predicted gene models. We then used a silk-gland transcriptome and a silk proteome to identify major silk components and verified the tissue specificity of the expression of individual genes.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on strains of Mycobacterium bovis, circulating in France, by the whole genome sequencing approach." Ciriac CHARLES

Appendix 1 Table showing the Mycobacterium bovis genome information used in this study in panel 1 The 87 genomes are from previous work (Hauer et al., 2019). The names of the genomes are highlighted with color to distinguish them within a previously defined M. bovis cluster. In Yellow Cluster I/Clonal Complex Eu3. In orange Cluster G/Family F9. In brown Cluster C/Family SB0134. In purple Cluster D/Clonal Complex Eu1. In pink the Cluster A/Family F4. In blue the Cluster F/Clonal Complex Eu2. In grey, the others. Appendix 2 Table showing the Mycobacterium bovis genome information used in this study in panel 3. The 187 genomes are of genotypes F7 and F15 (SB0821 and SB0832 respectively) which are two closely related genotypes. These genomes had already been sequenced before the start of the thesis work. Some were published with the work of Duault and collaborators and others have not yet been published (noted NA) (Duault et al., 2022). Appendix 3 Table showing the Mycobacterium bovis genome information used in this study in panel 4. The 227 genomes are of genotype SB0120-DHV. These genomes had already been sequenced before the start of the thesis work but are currently unpublished (noted NA in the columns "Date of deposit" and "Genbank biosample"). Appendix 4 Position of IS6110 insertion sites in the panel of Mycobacterium bovis strains from Pyrénées-Atlantiques (SB0821 and SB0832). The position of the start and end of IS6110 are determined with the ISMapper tool and the reference genome AF2122/97. Appendix 5 Position of IS6110 insertion sites in the Mycobacterium bovis strain panel of SB0120-DHV. Position of the start and end of IS6110 are determined with the ISMapper tool and the Mb3601 reference genome. Appendix 6 This figure from the Modenesi internship report represents a circular consensus phylogenetic tree of 300 strains of SB0120-DHV (Modenesi 2019). The strains in panel 3 are part of these 300 strains and were selected according to their sequencing quality, which explains the smaller number of strains retained (227). This tree is divided into 11 different colored clades. The posterior probability values (which correspond to the probability that these clades are true) determined with Beast (Drummond and Rambaut, 2007) are represented inside the tree.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on Mycobacterium bovis strains, circulating in France, by the whole genome sequencing approach", part "4. Sequencing of new complete genomes", Ciriac CHARLES

Annex S1: Sequencing metric of the 10 new genomes and obtained with fastqc. A: Metric provide to Illumina metric. B: metric provide to MinION metric. Annex S2: Pan-genomic study performed on 12 M. bovis complete genomes. The table indicates the genes accessory. “1” shows the presence of CDS and “0” his absence. Annex S3: Indels between the ten new complete genomes and Mb3601 using progressiveMauve. Annotation of these indels was performed with reference genome comparison for gap or with the annotation (with Prokka) of the new complete genome studied for insertion. IS6110 is marked in green. "Indel distribution" sheet shows the indel distribution on the M. bovis genome for the ten new complete genomes. Black arrows show the genomic region with the most of indel found. Annex S4: WgSNP analysis performed on 98 M. bovis. SNPs were annotated and selected according to their specificity to an M. bovis group described in Fig 5. The last common give information on the genetic impact of the SNP. The last sheet presents a graph of SNP number in genomic position. Annex S5: Alignments of the 12 M. bovis complete genomes.

opencc-zeroDec 2022View details →

Genome-wide RAD sequencing data suggest predominant role of vicariance in Sino-Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)

Disjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine relative roles of dispersal vs. vicariance in disjunctions. We studied phylogeographic pattern of the monotypic Conandron ramondioides (Gesneriaceae), which shows Sino-Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum (LGM), and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China + Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus Conandron. The sharp phylogenetic separation, ecological niche divergences among these three groups and the great number of private alleles in all populations sampled indicate a considerable time of independent evolution and suggest the need for a taxonomic survey to detect potentially overlooked taxa.

opencc-by-4.0Mar 2023View details →

SARS-COV-2 genomic sequences used as references for the NASCarD method

A set of 9 SARS-CoV-2 genome sequences used as reference in the NASCarD process.

opencc-by-4.0Apr 2023View details →

Draft Genome Sequences of Two Bacteriocin-Producing Enterococcus faecium Strains Isolated from Nonfermented Animal Foods in Spain

Raw sequences of two bacteriocin-producing Enterococcus faecium.

opencc-zeroMay 2023View details →

Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing

Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium Halotia branconii CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of generating complete quality genome sequences of microorganisms isolated from extreme intertidal environments, facilitating in-depth evaluation of ecological and taxonomic inferences.

opencc-by-4.0Apr 2023View details →

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

ncVarPred-1D3D: The data used for testing the inconsistency among genome sequence, epigenetic profile, and later, to show its relation to 3D chromatin structure can be found in sanity_check_data.tar.gz. Some trained model for noncoding mutation effect prediction (mapping genome sequence to epigenetic profile) can be found in CNN_MLP, CNN_GCN, CNN_RNN_MLP, CNN_RNN_GCN.tar.gz. The trained model for pathogenic variants prediction can be found in fewshot_pathogenic_model.tar.gz.  The training data can be found in training_data.tar.gz. Some noncoding variant effects prediction results, e.g. eQTL and pathogenic variants, can be replicated using the data shared in ncVar_data.tar.gz.

179 high quality metagenome-assembled genomes sequences and annotations

We analyzed seven sediment samples collected adjacent to ferromanganese nodules from the Clarion–Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean. Through deep metagenomic sequencing, assembly, and binning, we reconstructed 179 high quality metagenome-assembled genomes (MAGs). This archive contains these genomes sequences and annotations.

opencc-zeroJun 2023View details →

Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context

Molecular tools of species identification based on eNAs (environmental nucleic acids; eDNA and eRNA) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain "real-time" biodiversity estimates may be complicated by the differential persistence and degradation dynamics of the molecular template (eDNA or eRNA) and the barcode marker used. Here, we collected water samples over a 28-day period to comparatively assess species detection using eDNA and eRNA metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker (COI) and a nuclear rRNA marker (18S)—following complete removal of Arthropoda taxa in a semi-natural freshwater system. Our findings demonstrate that Arthropoda community composition was largely influenced by marker choice, rather than molecular template, individual microcosm, or sampling time point. Further, although eRNA may capture similar species diversity as the established eDNA method, this finding may be marker dependent. Although we found little to no difference in decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the ability of eNA-based metabarcoding to provide a strong correlation between true eNA copy numbers present in the environment and final read counts obtained (following the metabarcoding workflow). Collectively, our findings provide further support for the use of multi-marker assessments in metabarcoding surveys to unravel the broadest taxonomic diversity possible, highlight the limitations of eNA metabarcoding methods in providing accurate decay rate estimates, as well as establish the need for further comparative studies using both metabarcoding and single-species detection methods to assess the persistence and degradation dynamics of eNAs for a diverse range of taxa.

Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species

Raw data sets for the microbiologyOpen research article "Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species" including ClustalW Trees and the respective input file; canB 3.0 results; TYGS phylogenetic tree results; PGAP genome annotation files and Canu 2.0 assembly reports of the two genomes.

Massive Chinese domestic pigs provide missing sequences in reference genome and reveal non-coding sequence variations regulating gene expression across Eurasian boars

This dataset contains novel sequences in Chinese domestic pigs but is absent in Sscrofa 11.1 reference genome. The detailed information for each file is recorded in the README file.

Serratia fonticola EBS19 Whole genome sequence data fasta file annotated

Whole genome sequence data of Serratia fonticola EBS19 strain.

opencc-by-4.0Apr 2023View details →

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 epigenetic events Sei processed. The pretrained DeepSEA (PMID: 26301843) and reproduced DanQ (PMID: 27084946) can be found in SOTA.tar.gz.

Whole-genome capture and sequencing of Francisella tularensis directly from clinical samples

This dataset comprises: 1. The design of RNA oligonucleotide baits for Agilent Technologies’ SureSelect target enrichment - 54756 RNA oligonucleotide "baits" (120 bp each) designed to perform whole-genome capture and sequencing of Francisella tularensis directly from clinical samples (DNA) using Agilent Technologies’ SureSelect target enrichment system following the Illumina paired-end multiplexed sequencing library protocol. RNA oligonucleotide “baits” were designed to span the Francisella tularensis chromosome and plasmid, accounting for the genetic variability among publicly available genome sequences. All resulting sequences were BLASTn searched against the Human Genomic + Transcript database to excluded homologous sequences to the human genome. Overall, a total of 54756 RNA probes were generated and this custom bait library was then uploaded to the SureDesign software (https://earray.chem.agilent.com/suredesign) and synthesized by Agilent Technologies. 2. Genome assemblies of 17 Francisella tularensis samples generated in the context of validation and application of SureSelect target enrichment for Whole-genome capture and sequencing of Francisella tularensis directly from clinical samples   File “Ft_assembly_metadata.xlsx” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers. The archive “Ft_assemblies.zip” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. More details can be found in the following publication: (available soon)