Find research datasets worth reusing

openmit-licenseMay 2022View details →

Queries and graphs for sequence to graph alignment method evaluation

The tar contains two directories for queries and graphs used to evaluate the sequence to graph alignment methods.

opencc-zeroJun 2022View details →

FASTA file of sequences of identified proteins in Anastrepha ludens reproductive tissues

Seminal fluid proteins (Sfps) modify female phenotypes and have wide-ranging evolutionary implications on fitness in many insects. However, in the Mexican fruit fly, Anastrepha ludens, a highly destructive agricultural pest, the functions of Sfps are still largely unknown. To gain insights into female phenotypes regulated by Sfps, we used nano liquid chromatography mass spectrometry to conduct a proteomic analysis of the soluble proteins from reproductive organs of A. ludens. The proteins predicted to be transferred from males to females during copulation were 100 proteins from the accessory glands, 69 from the testes, and 20 from the ejaculatory bulb, resulting in 141 unique proteins after accounting for redundancies from multiple tissues. These 141 included orthologs to Drosophila melanogaster proteins involved mainly in oogenesis, spermatogenesis, immune response, lifespan, and fecundity. In particular, we found one protein associated with female olfactory response to repellent stimuli (Scribble), and two related to memory formation (aPKC, Shibire). Together, these results raise the possibility that A. ludens Sfps could play a role in regulating female olfactory responses and memory formation and could be indicative of novel evolutionary functions in this important agricultural pest.

SARSCoV2 and Influenza A & B sequence dataset

COMPUTATIONAL EXPLORATION TOWARDS UNIVERSAL VACCINES FOR INFLUENZA AND CORONAVIRUSES Thesis by Menno Van Damme This dataset contains SARS-CoV-2 and Influenza A & B sequences downloaded from NCBI, their metadata and their alignments. It also contains the results from conservation analysis, phylogenetic analysis and RNA secondary structure prediction. The thesis text and the python scripts used are available at: https://github.com/menvdamm/Thesis Note: the SARS-CoV-2 dataset is split into three, in order to use the scripts these 3 files have to be unzipped inside a folder called 'Data' inside of the working directory. For SARSCoV2 the original data downloaded from NCBI could not be included because of the file size.

opencc-by-4.0Apr 2022View details →

Data for for Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

Datasets accompanying the paper https://doi.org/10.1101/2021.10.18.464684

Integration of single-cell RNA-sequencing data across tissues and cancer types towards immune cell characterization

To better understand dendritic cell states and subtypes, we collected individual single-cell RNAseq datasets from various studies and further integrated, batch corrected, and reprocessed the data using Besca (https://github.com/bedapub/besca). The following files are included: 1) study_table_integrated_DCs.xlsx - contains a list of studies from where the datasets were gathered. 2)  int_dcs.raw.h5ad - An anndata object file containing the combined raw single-cell counts for DCs from individual studies. The datasets were joined based on the union of variables. 3) intersection_genes_integrated_dcs.tsv - List of genes if the datasets were joined based on the intersection of variables. These variables were used in the subsequent analyses. 4) int_dcs.annotated.h5ad - An anndata object file containing single-cell logarithmized counts for DCs data that have been integrated and reprocessed. The rows of the file contain cells, and the columns contain highly variable genes. A sparse matrix containing the logarithmized counts from all the genes (from the intersection genes integrated dcs.tsv file) can also be found (adata.raw.X) in the object. In the observations, cell-type annotation is available at three different hierarchal levels. This data was further used to produce results for the publication (https://jitc.bmj.com/content/10/6/e004268) on the effects of Toll-like receptor 8 agonists on conventional DCs.

opencc-zeroJun 2022View details →

Data from: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

opencc-by-4.0Feb 2022View details →

Modeling the Organic Carbon Oxidation and Redox Sequence under the Partial- Equilibrium Approach: a Discussion by means of a Semi-Analytical Solution

Filename: Analytical_solution.xls File format: Excel Description: It contains the calculation of the analytical model, programmed by means of excel. The sheet "advection" contains the calculation of the advection model and the sheet "diffusion" that of the diffusion model. The sheet "Phreeqc results" contains the results of the Phreeqc batch model (see Batch.pqi). Input data are highlighted in yellow. Filename: Batch.pqi File format: Phreeqc Description: It contains the input file for the calculation of the batch model by Phreeqc. It requires the Phreeqc database file Phreeqc.dat Filename: PEA_om_adv.pqi File format: Phreeqc Description: It contains the input file for the numerical calculation of the advection model by Phreeqc using the PEA (Partial Equilibrium Assumption). It requires the Phreeqc database file Phreeqc.dat Filename: PEA_om_dif.pqi File format: Phreeqc Description: It contains the input file for the numerical calculation of the diffusion model by Phreeqc using the PEA (Partial Equilibrium Assumption). It requires the Phreeqc database file Phreeqc.dat Filename: KIN_om_adv.pqi File format: Phreeqc Description: It contains the input file for the numerical calculation of the advection model by Phreeqc using the fully kinetic approach. It requires the Phreeqc database file PhreeqcKIN.dat Filename: KIN_om_dif.pqi File format: Phreeqc Description: It contains the input file for the numerical calculation of the diffusion model by Phreeqc using the fully kinetic approach. It requires the Phreeqc database file PhreeqcKIN.dat Filename: phreeqc.dat File format: Phreeqc database Description: It contains thermodynamic data for the batch model (see Batch.pqi) and the PEA models (see PEA_om_adv.pqi and PEA_om_dif.pqi). It is the default thermodynamic database of Phreeqc, dat), from which we removed ammonium to avoid the unrealistic reduction of NO3- and N2 to NH4+ Filename: phreeqcKIN.dat File format: Phreeqc database Description: It contains thermodynamic data for the fully kinetic models (see KIN_om_adv.pqi and KIN_om_dif.pqi). It is the default thermodynamic database of Phreeqc, dat), from which we removed the relevant equilibrium redox reaction, so that they can be treated kinetically.

opencc-zeroOct 2019View details →

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for ~3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic dataset for cetaceans, spanning 6,527,596 aligned base pairs and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among ocean dolphins, especially the problematic subfamily Delphininae, which includes the common and bottlenose dolphins. We performed Bayesian estimation of species divergence times using MCMCtree, integrating recently described fossils as calibration points (e.g., Mystacodon selenensis) that have not been used before. Integration of new fossil dates in the context of autocorrelated rates indicate that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene.

16S rRNA sequence database

This 16S rRNA database was curated for honeybee gut microbiome.

Automated inference of sequences of operations in RESTful APIs with deep reinforcement learning - replication package

This directory contains the replication package of the article entitled "Automated inference of sequences of operations in RESTful APIs with deep reinforcement learning". Please note that this is NOT a real publication or scientific report, but a project created for the purpose of learning the basic concepts of research by emulating the process of creating an article.

opencc-zeroDec 2018View details →

Data from: An integrated genotyping-by-sequencing polymorphism map for over 10,000 sorghum genotypes

[No abstract entered]

opencc-zeroDec 2013View details →

Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology

Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci – Stepwise Threshold Clustering (STC) – that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.

opencc-zeroJul 2022View details →

ITS and LSU sequences, phylogenetic trees

Russula kashmiriana sp. nov (subg. Tenellula, sect. Laricinae) has been collected and described from Himalayan coniferous forest of Azad Jammu and Kashmir (AJ&K), Pakistan. The taxon is characterized by bright reddish orange pileus with cracked margins and obvious reddish orange circle on the pileus, yellow context and light olive to yellowish amyloid basidiospores. Micro and macroscopic features along with molecular phylogenetic analysis based on large subunit (LSU) and internal transcribed spacer (ITS) sequences data confirmed the status of Russula kashmiriana as a distinct species. AJ&K, LSU, Phylogeny, Russulaceae.

opencc-by-4.0Apr 2022View details →

Xcc BrA1 re-sequenced genome contigs, annotation file and Trinitiy De-nove assembled DEG's

Assembled genome contigs of Xcc strain BrA1 (Behlau et al 2017) which was re-sequenced by our lab and used in a copper stress Transcriptome study. A hybrid RNA-seq analysis pipeline was used and the DEG Trinity De-novo assembled transcripts are also included.

16s rRNA and copLAB partial sequences of copper resistant Xanthomonas spp. isolated from agrochemical impacted crucifer fields in Trinidad

Sanger sequence generated partial sequences of copLAB genes present in copper resistant Xanthomonas spp associated with leaf lesion and 16s rRNA sequences used for bacterial genera identification. Part of an upcoming manuscript, will be linked within document.

Fast Intratumor Heterogeneity Inference from Single-Cell Sequencing Data (simulated data - Extended Data Figures)

This data repository contains simulated data used for benchmarking HUNTRESS against the existing alternative tools. Results of the benchmarking are shown in Extended Data Figures 1-10 of the paper "Fast Intratumor Heterogeneity Inference from Single-Cell Sequencing Data" (to appear in Nature Computational Science).

RNA sequencing analysis of CAF treated by colon cancer cell-derived exosomes

In this study, we analyzed differentially expressed genes by obtaining gene expression values through transcriptome sequencing of Homo sapiens, and performed functional classification and gene annotation for significant genes based on gene ontology and pathway information. After the pre-processed trimmed reads were mapped to a known reference genome using the HISAT2 program, transcript assembly was performed through the StringTie program. As a result, expression profile values were obtained for each sample for the known transcript, and read count, based on transcript/gene Fragment per Kilobase of transcript per Million mapped reads (FPKM), Transcripts per Kilobase (TPM) Million) values have been summarized. This value was subjected to DEG (Differentially Expressed Genes) analysis using edgeR for comparison combinations (HT-29_Exo-CAF vs. CTL_PBS-CAF, LoVo_Exo-CAF vs. CTL_PBS-CAF, and SW480_Exo-CAF vs. CTL_PBS-CAF), and genes that satisfies the condition |fc|>=2 & exactTest raw p-value<0.05 in at least one comparison combination Dogs were extracted. Transcriptome resequencing data was used to compare expression profiles between comparable samples. Gene Ontology Enrichment analysis was performed using the g:Profiler tool (https://biit.cs.ut.ee/gprofiler/) for a list of genes with significant expression level differences. GO_stat is the result of organizing the associated gene and test stat based on term_id. GO_genes is the result of arranging the associated term_id and DEG analysis result stat based on the gene.

Supplementary Data for "Phosphorus variations in volcanic sequences reveal the linkage between regional tectonics and terrestrial biota evolution" in G-Cubed.

Supplementary data tables for Ma et al. (2022) associated with the paper entitled "Phosphorus variations in volcanic sequences reveal the linkage between regional tectonics and terrestrial biota evolution" published in G-Cubed.

opennotspecifiedNov 2017View details →

Distribution. Until recently considered to occur in C & NE Angola and S & SE DR Congo, but based on cytochrome-b sequences, Bryja and colleagues in 2014 extended the range to include the NW region and the Eastern Arc Mts of Tanzania, much of NE Zambia, and Malawi; also re- corded from a single locality in extreme NW Zambia. in Muridae

Distribution. Until recently considered to occur in C & NE Angola and S & SE DR Congo, but based on cytochrome-b sequences, Bryja and colleagues in 2014 extended the range to include the NW region and the Eastern Arc Mts of Tanzania, much of NE Zambia, and Malawi; also re- corded from a single locality in extreme NW Zambia.