Find research datasets worth reusing

RNA-sequencing of meningioma cell lines with miRNA constructs

RNA-sequencing of meningioma cell lines with miRNA constructs.

What controls active faulting in Tertiary and Quaternary sequences ?

Structural, geomechanical and XRD datasets obtained from outcrop investigations of Galera Fault zone located in the Guadix-Baza basin, SE Spain is presented here.

Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis

Gaussian input and output files required to reproduce the results and analyses in the work. Code required to conduct analysis and representation.

Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16- 3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment.

Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16-  3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment. Determined from Illumina shotgun genomic sequencing datasets, mapping and analyses vs the reference genome of the strain https://www.ncbi.nlm.nih.gov/nuccore/NC_007795.1/

opencc-by-4.0Feb 2024View details →

Oxford Nanopore sequencing for comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity

The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes, or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, and for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here, we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative, and unbiased identification of most eukaryotic species.

NSRC-Search: Efficient searching for similar protein sequences of non-standard amino acid composition

This research was funded by the National Science Centre in Poland (grant number 2021/41/N/ST6/01919)

Data required for "Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences"

In the early 1900s,mutation breeding to select varieties with desirable traits using  spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of NGS technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using next-generation sequencing (NGS) to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a shortchain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.

Sequencing data for Flp-In T-Rex HeLa PINK1 CRISPR/CAS9 knock-out (CVCL_D5JI)

PCR and sequencing data (.ab1 and .seq files) for CRISPR-Cas9 PINK1 knockout HeLa cells (clone 3C9) described in <a title="doi link" href="https://doi.org/10.1098/rsob.210264">doi.org/10.1098/rsob.210264</a>. Knock-out generated using the following guides (targeting exone 2), available from MRC-PPU Reagents and Services, University of Dundee: DU52528 and DU52530 (CRISPR Project #CR252). This cell line has been deposited to Cellosaurus: CVCL_D5JI.

A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

This is a public repository containing secondary datasets described in the publication <a href="https://doi.org/10.26508/lsa.202302481">"A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing"</a>. Primary data for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955, and include the following sequencing datasets: REH cell line: <ul> <li>PacBio WGS</li> <li>ONT Ultralong WGS</li> <li>Illumina short-read PCR-free WGS</li> <li>IsoSeq RNA-seq</li> <li>Illumina short-read RNA-seq</li> </ul> GM12878 cell line: <ul> <li>Illumina short-read RNA-seq</li> </ul> This dataset includes the following files: Depth of Coverage analysis <ul> <li>Output from `samtools coverage`: samtools.coverage.illumina.txt, samtools.coverage.ont.txt, samtools.coverage.pb.txt</li> <li>Output from `copycat` (binned coverage): copycat.ont.coverage.10kb.csv, copycat.pb.coverage.10kb.csv, copycat.pcrfree.coverage.10kb.csv</li> </ul> Structural Variant (SV) callsets <ul> <li>Raw: illumina.tiddit.vcf, ont.sniffles.vcf, pb.sniffles.vcf</li> <li>Filtered: REH.svs.filtered.csv</li> </ul> SNV callsets <ul> <li>Filtered and annotated: REH.mutect.filtered.ann.vcf.gz</li> </ul> Fusion gene callsets <ul> <li>Short-read: GM12878.fusionreport.txt, illumina.all.txt, illumina.filtered.csv, REH.arriba.fusions.tsv, REH.fusioncatcher.fusion-genes.txt, REH.pizzly.txt, REH.squid.fusions.annotated.txt, REH.starfusion.abridged.tsv, REH.pdf</li> <li>Long-read: cupcake.long.csv, cupcake.std.csv, jaffa_results.csv</li> <li>Filtered: REH.fusions.filtered.csv  </li> </ul>

Synthetic Rabbit Plenoptic Test Sequence

The test sequence "Synthetic Rabbit" is provided by Sarah Fachada, Daniele Bonatto, Gauthier Lafruit, Mehrdad Teratani, members of the LISA department, EPB (Ecole Polytechnique de Bruxelles), ULB (Universite Libre de Bruxelles), Belgium. <h3>License: </h3> CC BY-NC-SA ONLY Available for Academic Usage  <h3>Terms of Use: </h3> Anykind of publication or report using this sequence should refer to the following references. [1] Sarah Fachada, Daniele Bonatto, Gauthier Lafruit, Mehrdad Teratani, "Synthetic Rabbit Plenoptic Test Sequence", 2024. @misc{fachada_syntheticrabbit_2024,     title = {{Synthetic} {Rabbit} {Plenoptic} {Test} {Sequence}},     author = {Fachada, Sarah and Bonatto, Daniele and Lafruit, Gauthier and Teratani, Mehrdad },     month = mar,     year = {2024},     doi = {10.5281/zenodo.10894522} } <h3>Production:</h3> Laboratory of Image Synthesis and Analysis, LISA department, Ecole Polytechnique de Bruxelles, Universite Libre de Bruxelles, Belgium. <h3>Content:</h3> This dataset contains a test scene acquired with synthetic plenoptic cameras and a line of 51 pinhole images.  The dataset structure is the following: <ul> <li>"cameras.json" which is a json file with the parameters of the plenoptic cameras and of the pinhole cameras located at the main lens centers;</li> <li>"cameras_nav.json" which is a json file with the parameters of a line of 51 pinhole cameras;</li> <li>three folders, "Keplerian", "R5", "R8", each corresponding to a different plenoptic camera models, inspired respectively from Tsinghua University’s camera [1], Raytrix R5 and R8 models [2], each containing: <ul> <li>a "color" folder with images in plenoptic format. The images are in 4 versions, without degradation, with blur due to multi-focus, with luminance decay and with blur and luminance decay;</li> <li>a "depth" folder with depth images associated to the color plenoptic image. The depth maps are in millimeters, from the main lens. We provide the ground truth depth maps, and depth maps obtained from Plenoptic Toolbox [3] and LLMV [4] disparity estimations;</li> <li>a "pinhole" folder with the pinhole image placed at center of the main lens and its associated depth map;</li> <li>a "navigation" folder with 51 color pinhole images placed every two millimeters.</li> </ul> </li> </ul> <h3> References and links:</h3> [1] X. Sun, X. Jin, T. Zhong, et P. Wang, "[MPEG-I Visual] A New Self-designed Focused Plenoptic Camera and the Captured Video Sequence “Boys” [m46259]", Marrakesh, Morocco, janv. 2019. doi: ISO/IEC JTC1/SC29/WG11 MPEG2019/M46259. [2] Raytrix, https://raytrix.de/ [3] L. Palmieri, R. Koch, et R. O. H. Veld, "The Plenoptic 2.0 Toolbox: Benchmarking of Depth Estimation Methods for MLA-Based Focused Plenoptic Cameras", in 2018 25th IEEE International Conference on Image Processing (ICIP), IEEE, 2018. doi: 10.1109/ICIP.2018.8451073. [4] D. Bonatto et al., "Multiview from Micro-Lens Image of Multi-Focused Plenoptic Camera", in 2021 International Conference on 3D Immersion, Brussels, Belgium, déc. 2021, p. 8. doi: 10.1109/IC3D53758.2021.9687243.   <h3>Acknoledgements:</h3> Sarah Fachada is a postdoctoral researcher of the FNRS This work was supported in part by the FER 2021 project (1060H000066-FAISAN), Belgium;  in part by the Emile DEFAY 2021 project (4R00H000236), Belgium;  and in part by the FER 2023 project (1060H000075), Belgium.

NASTRA: Accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm

Forensic short-tandem repeats (STR) genetic markers are multi-allelic and widely utilized for individual identification, kinship testing, and cell-line authentication. Nanopore sequencing, known for its portability, is emerging as a promising approach for STR typing, facilitating real-time and in-field testing. However, its efficacy is often hampered by sequencing noise. Previous methods rely on alignment-based genotyping, necessitating known alleles, which limits their applicability to unknown alleles. Here, we introduced NASTRA, an innovative allele reference-free tool for precise germline analysis of STR genetic markers. NASTRA incorporates a recursive algorithm to infer repeat structures of allele sequences using only known repeat motifs. Our tests, conducted on 80 individual samples and 8 DNA standards, have demonstrated NASTRA's exceptional 100% accuracy in genotyping nearly all diploid STRs across various multiplex kits and flow cells. It surpasses alignment-based methods in accuracy and speed. In a paternity testing case study, NASTRA accurately identified three relationships among six individuals within an 18-minute sequencing duration. These results underscore NASTRA's ability to perform STR analysis on both NGS and nanopore sequencing platforms, significantly enhancing the utility of nanopore sequencing in relevant applications.

opencc-zeroApr 2024View details →

16S rDNA sequencing data for characterizing the endosymbionts of leaf curl plum aphid ( Brachycaudus helichrysi) clones

Asexual lineages often exhibit broad distributions and can thrive in extreme habitats compared to their sexual counterparts. Several hypotheses can be proposed to explain this pattern. Asexual lineages could be versatile genotypes with wide environmental tolerance, enabling their dispersal and persistence across large geographic areas. Alternatively, asexual genotypes could be ecological specialists that thrive in specific environments and outcompete relatives colonizing distantly related areas with similar conditions in the process. Several aphid species feature widespread obligate asexual lineages, commonly known as "superclones". Yet it is often unknown whether these clones are widespead ecological generalists or successful specialists. To explore these hypotheses, we examined climatic niche differentiation among six globally distributed obligate asexual lineages of the cosmopolitan aphid pest, Brachycaudus helichrysi. To insure that we were investigating the aphid genotype niche and not a by-product of their association with endosymbionts mediating thermal tolerance, we first verified that clones hosted similar endosymbiont communities. Subsequently, we conducted multivariate analyses on clone occurrence data on a worldwide scale. Our results revealed that despite their global distribution, B. helichrysi superclones occupy different climatic niches. This study represents the first evidence that aphid superclones distribution can be mediated by distinctive ranges of climatic tolerance.

opencc-by-4.0Jan 2024View details →

MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

This repository contains the data required to run the example notebooks and to reproduce the figures from the paper :  <div> <div>MUFFIN : A suite of tools for the analysis of functional sequencing data</div> </div> <div>Pierre de Langen, Benoit Ballester</div> <div>bioRxiv 2023.12.11.570597; doi: <a href="https://doi.org/10.1101/2023.12.11.570597" target="_blank" rel="noopener">https://doi.org/10.1101/2023.12.11.570597</a></div> <div> </div> <div>Source code is located here :</div> <div><a href="https://github.com/pdelangen/Muffin" target="_blank" rel="noopener">https://github.com/pdelangen/Muffin</a></div> <div> </div> <ul> <li>10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.</li> <li>genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)</li> <li>GO_files/ contains gene set information retrieved from the g:ProfileR website.</li> <li>immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.</li> <li>tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.</li> <li>scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.</li> </ul> <div> </div>

Derived Protein Sequence Data From Kaggle

It is the dataset containing protein sequence and its associated go-terms, used for priliminary training process

opencc-zeroApr 2024View details →

Data from Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches

Background The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates. Results Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson's correlation and 0.94 Spearman's correlation to these benchmarks. Application of a novel estimation approach, fixed length taxonomic ratios, improved quantification accuracy of simulated human gut microbial communities when compared to estimates of mean or median coverage. Conclusions We investigate the possible strengths and weaknesses of applying the RMS technique to profiling microbial communities via simulations with readsynth. The choice of restriction enzymes and size selection steps in library prep are non-trivial decisions that bias downstream profiling and quantification. The simulations investigated in this study illustrate the possible limits of preparing metagenomic libraries with a reduced representation sequencing approach, but also allow for the development of strategies for producing and handling the sequence data produced by this promising application.

Fragmented sequences for mosquito-associated viruses and other viruses

Fragmented fasta sequences associated with the manuscript Predicting novel mosquito-associated viruses from metatranscriptomic dark matter

Automatic message sequence chart creation from simulation run of the proposed parametric colored Petri net model of the Chandy-Lamport algorithm

These videos show the creation of two message sequence charts from simulation runs of the proposed parametric colored Petri net model of the Chandy-Lamport algorithm using the CPN tool with three constituting processes. Message Sequence Chart of  Parametric Model With 3 Processes via Automatic Simulation Run_SuppInfo.mp4: This video shows the automatic generation of a message sequence chart of the proposed parametric colored Petri net model of the Chandy-Lamport distributed global snapshot algorithm using the CPN tool version 4.0.0. The number of constituting processes is parametric in the model and was set to three. The video was generated using the authors' updated CPN tool extension server. The automatic simulation run of the model has been used to create this video. The CPN tool randomly selects the enabled transition at each step in an automatic simulation run. Message Sequence Chart of Parametric Model With 3 Processes via Step-By-Step Simulation Run_SuppInfo.mp4: This video shows the automatic generation of a message sequence chart of the proposed parametric colored Petri net model of the Chandy-Lamport algorithm in a step-by-step simulation run with our updated extension server of the CPN tools version 4.0.0. The number of constituting processes is parametric in the model and was set to three. We manually fired our selected enabled transition of the model to create this video.

opencc-zeroApr 2023View details →

Whole genome sequencing (WGS) data from invasive pine sawfly Diprion similis

Biological introductions are unintended "natural experiments" that provide unique insights into evolutionary processes. Invasive phytophagous insects are of particular interest to evolutionary biologists studying adaptation, as introductions often require rapid adaptation to novel host plants. However, adaptive potential of invasive populations may be limited by reduced genetic diversity—a problem known as the "genetic paradox of invasions". One potential solution to this paradox is if there are multiple invasive waves that bolster genetic variation in invasive populations. Evaluating this hypothesis requires characterizing genetic variation and population structure in the invaded range. To this end, we assemble a reference genome and describe patterns of genetic variation in the introduced white pine sawfly, Diprion similis. This species was introduced to North America in 1914, where it has rapidly colonized the thin-needled eastern white pine (Pinus strobus), making it an ideal invasion system for studying adaptation to novel environments. To evaluate evidence of multiple introductions, we generated whole-genome resequencing data for 64 D. similis females sampled across the North American range. Both model-based and model-free clustering analyses supported a single population for North American D. similis. Within this population, we found evidence of isolation-by-distance and a pattern of declining heterozygosity with distance from the hypothesized introduction site. Together, these results support a single-introduction event. We consider implications of these findings for the genetic paradox of invasion and discuss priorities for future research in D. similis, a promising model system for invasion biology.

opencc-zeroApr 2024View details →

Symbiodiniaceae ITS2 sequences from reef corals in St. John, U.S. Virgin Islands

Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from 9 species were marked and sampled in 2017, and following hurricanes in September 2017, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes and the onset of stony coral tissue loss disease. While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.