Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,584
datasets available to search
ShareScore release 0.9.0
Dataset results
3,584 results for “genomic analysis”
FIGURE 1 in Transfer of the marine red alga Erythrocystis saccata (Rhodomelaceae, Rhodophyta) to the tribe Streblocladieae inferred from organellar genome analysis
FIGURE 1. Erythrocystis saccata growing epiphytically on Laurencia pacifica from Stillwater Cove, Pebble Beach, California, USA (UC 2085026). The arrow indicates the specimen analyzed in this study. White bar = 2 cm.
Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights into Phylogenetic Relationships of Onagraceae
<p>This is all the alignments which used to constructed a phylogenetic tree in our study about Onagraceae. The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, which comprises 22 genera widely distributed from boreal to tropical areas. In the present study, we report and characterize the complete chloroplast genome sequences of 13 species in <em>Circaea</em>,<em> Chamaenerion</em>, and <em>Epilobium</em> using a next-generation sequencing method. We also retrieved plastome sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete plastomes of Onagraceae showed a typical quadripartite structure and encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The results show that chloroplast genomes are basically conserved in gene arrangement across the family. Whereas, a large segment of inversion was detected in the LSC region of all samples in the<em> Oenothera </em>subsect. <em>Oenothera</em>. An inverted repeat (IR) contraction was found in <em>Circaea</em> and<em> Ludwigia </em>samples. We also compared chloroplast genomes across the Onagraceae samples and revealed similarities in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference (BI) methods. The generic relationship of Onagraceae was well resolved by the complete plastome sequences, showing potential value in inferring phylogeny within the family. <em>Oenothera </em>phylogeny was better resolved than other densely sampled genera. Biparental transmission may be the main cause of higher variation in the genus<em> Oenothera</em>.</p>
Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist
<p>Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we<span> generated a genome assembly for the free-living metamonad <i>Carpediemonas membranifera</i> and</span> carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, <i>Carpediemonas </i>species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. <i>Carpediemonas</i> species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.</p>
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis (yeast-pb-pbsim2)
<p><strong>yeast-pb-pbsim2</strong></p> <p>Simulated PacBio CLR (P6 C4 model) reads used in the BLEND paper submission. Generated using PBSIM2 (see the yeast-pb-pbsim2/pbsim200x/pbsim.sh file)</p>
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis (yeast-ont-pbsim2)
<p><strong>yeast-ont-pbsim2</strong></p> <p>Simulated ONT reads (R9.5 model) used in the BLEND paper submission. Generated using PBSIM2 (see the yeast-ont-pbsim2/pbsim100x/pbsim.sh file)</p>
Minimizer collision statistics (BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis)
<p>This dataset includes the statistics for the minimizers that generate the same hash value (i.e., collisions). The hash values are generated using a low-collision hash function and the SimHash technique in BLEND.</p> <p> </p> <p>*collision_stats.txt files include the overall collision statistics for a tool and configuration of the tool (i.e., the number of colliding minimizer pairs with a certain edit distance and their ratio to all number of collisions). For example blend_n3_collision_stats.txt shows the statistics for BLEND where the number of neighbors is set to 3 when running BLEND.</p> <p>_sim.csv files include all minimizer pairs with the same hash value and the edit distance between them.</p> <p> </p>
K-mer collision statistics (BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis)
<p>This dataset contains 1,077 FASTA files and CSV files. Each FASTA file includes 25-character long sequences similar to each other.</p> <p>We have a CSV file for each tool (i.e., minimap2 and BLEND) and configuration (i.e., different number of neighbors in BLEND). CSV files include the non-identical k-mer pairs (16-mers) that generate the same hash value (i.e., collisions). These k-mers are extracted from sequences that are similar to each other. In each line, we show the hash value of the k-mers, the actual sequene pairs that the k-mers are extracted from, k-mer pairs that generate the same hash value, and the edit distance between these k-mers.</p> <p> </p>
Phylogenetic Analysis Based on the Complete Mitochondrial Genomes of Eight Nymphalidae Species (Lepi-doptera: Papilionoidea)
<p>Table S1: Basic sequence characteristics of mitochondrial genomes of eight newly sequenced species in Nymphalidae;</p> <p>Table S2: Base composition, AT content, AT-skew, GC-skew and total length (bp) of 105 species in all three codon positions, codon position 1, codon position 2 and codon position 3 in this study. The species highlighted in red are the ones that were sequenced;</p> <p>Table S3:<strong> </strong>Taxonomic information and GenBank accession numbers for 105 mitogenomes in Nymphalidae selected for characteristics and phylogenetic analysis in this study.</p>
BGCFlow Analysis of Saccharopolyspora Genomes
<p>The dataset contains genome mining analysis from publicly available Saccharopolyspora genomes.</p>
Genome-Wide Association Studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity
<p>Postembryonic primary root growth relies on meristems that harbour multipotent stem cells that produce new cells that will duplicate and provide all the different root cell types. <em>Arabidopsis thaliana</em> primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth. We used 639 accessions from nine different studies and performed different GWAS tests ranging from single studies and pairwise analysis with high correlation associations, analyzing the same number of accessions in different studies to using the daily data of the root growth kinetic of the same research. We found that primary root growth changes were associated with 41 genomic loci, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown of genes associated with two of these loci: a gene that participates in Trans-acting siRNAs (tasiRNAs) processing <em>Suppressor of Gene Silencing</em> (<em>SGS3</em>) and a gene with a Sterile Alpha Motif (SAM) confirmed their participation as repressors of primary root growth. As none has been shown to participate in this developmental process before, our GWAS analysis identified new genes that participate in primary root growth. Overall, our findings provide novel insights into the genomic basis of root development and further demonstrate the usefulness of GWAS meta-analyses in non-human species.</p>
FIGURE 2. A in Lessons from the genomic analysis of Hesperiidae (Lepidoptera) holotypes in the MIZA collection (Maracay, Venezuela)
FIGURE 2. A female of Jemadia demarmelsi NVG-20054H05 from Venezuela, Bolívar, Gran Sabana, Kavanayén, 1350 m, 05-Mar-2017, M. Costa leg.
Fig. 6 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 6. Heatmap representing organ specific significantly enriched genes corresponding to (A) Isosteroidal alkaloid biosynthesis, (B) Sucrose and starch metabolism, (C) UGTs and CYPs, (D) aquaporins, (E) ABC transporters, (F) Transcription factor and Transposable elements. The red-blue scale represents positive enrichment (red) and negative enrichment (Blue) of transcripts. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 5. Significantly enriched transcripts (nodes) in predicted interactome network. (A) Steroidal alkaloid biosynthesis pathways (B) Isopentenyl diphosphate biosynthesis pathway, (C) Sucrose and starch metabolic pathways and (D) Aquaporins. The nodes encircled in red color represents higher enrichment in the bulb while the nodes encircled in grey and blue represents higher enrichment in arial organs (leaf and stem). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 7 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 7. qRT-PCR expression-based validation of RNA-seq data using potential 20 genes involved in isosteroidal alkaloid biosynthetic pathway. (A) Bulb vs. Leaf, (B) Leaf vs. Stem and (C) Bulb vs. Stem.
Fig. 3 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 3. Significant KEGG pathway enrichment analysis in tissues from aerial organs (leaf & Stem) and bulb. The green colour enrichment indicates higher expression in aerial tissue while pink represents higher enrichment in bulb. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 4. Transcriptional protein-protein interactome (PPIN) prediction in F. roylei along the network statistics. (A) Overall prediction of PPI network based on significantly differential expressed transcripts. Spatial PPI network prediction of significantly enriched transcripts in (B) Bulb, (C) Leaf and (D) Stem.
Fig. 1 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 1. Summary of organ specific spatial transcriptome sequencing in F. roylei. (A): Overall quality filtering of sequenced reads; (B): Tissue specific high quality filtered reads obtained after removing low quality/adaptor contaminated sequences; (C): Assembly statistics details; (D): Venn diagram representing functional annotation with six different public protein databases.
Fig. 8 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 8. Representation of isosteroidal alkaloid biosynthesis pathway in F. roylei and heat map representing expression of genes in Stem, Leaf and Bulb tissue using red-blue scale (red: positive enrichment and Blue: negative enrichment of transcripts). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 2. Clustering of 2488 significant differentially expressed transcripts in leaf, stem and bulb in F. roylei (A) sub-cluster 1 represent transcripts with significant higher expression in bulb; (B): Sub-cluster 2 in Stem and (C): Sub-cluster 3 in leaf; (D): Pearson's correlation of organ specific significant differentially expressed clustered transcripts in leaf, stem and bulb tissues.
Fig. 7 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 7. Expression profiles analysis of OsFBNs under different temperature stresses. Eleven OsFBN genes in rice were detected for their transcript levels in leave tissues of seedlings at the three-leaf stage with different time intervals after the 35 ̊C (heat stress) and 6 ̊C (cold stress) stresses in the growth chamber, separately. The OsUBQ gene was used as a normalization control; data was measured as the mean values ± SD of three replicates, respectively.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.