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832 results for “genomics and transcriptomics”
Processed Saccharomyces cerevisiae transcriptomics and genomics data for machine learning
<p><strong>Genomic data including open reading frame (ORF) boundaries of Saccharomyces cerevisiae C288 was obtained from the Saccharomyces Genome Database (<a href="https://www.yeastgenome.org/">https://www.yeastgenome.org/</a>) (<a href="http://paperpile.com/b/QmuOBv/gg2yy">Cherry, J. M. et al. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 40, D700–5 (2012)</a>) and published data (<a href="http://paperpile.com/b/QmuOBv/g4EbQ">Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033–1037 (2009)</a>, <a href="http://paperpile.com/b/QmuOBv/uJqAw">Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008)</a>). </strong><strong>Coding regions were extracted based on ORF boundaries and codon frequencies were normalized to probabilities. Processed raw RNA sequencing Star counts were obtained from the Digital Expression Explorer V2 database (<a href="http://dee2.io/index.html">http://dee2.io/index.html</a>) (<a href="http://paperpile.com/b/QmuOBv/LCGD">Ziemann, M., Kaspi, A. & El-Osta, A. Digital expression explorer 2: a repository of uniformly processed RNA sequencing data. GigaScience vol. 8 (2019)</a>) and filtered for experiments that passed quality control. Raw mRNA data were transformed to transcripts per million (TPM) counts and genes with zero mRNA output (TPM < 5) were removed. Prior to modeling, the mRNA counts were Box-Cox transformed.</strong></p>
Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology
<p>Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in <i>TMEM106B</i> (p-value < 5´10<sup>-8</sup>, rs1990620<sup><span><span>G</span></span></sup>) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together,<b> </b>our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.</p>
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"
<p>This is the directory containing input data necessary to reproduce analyses presented in the manuscript:</p> <blockquote> <p><strong>CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells</strong><br> Shadi Darvish Shafighi, Szymon M Kiełbasa, Julieta Sepúlveda Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan Kloet, Hendrik Veelken, Cornelis A.M. van Bergen, Ewa Szczurek</p> </blockquote>
Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic and reliably scored after genotyping of 105 individuals from three locations in the Eastern Atlantic Ocean. These markers will be valuable for future studies on population genetic structure assessment and for product tracing.
Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment
<p>Ocean warming favors pelagic tunicates, such as salps, that exhibit increasingly frequent and rapid population blooms, impacting trophic dynamics and composition and human marine-dependent activities. Salp blooms are a result of their successful reproductive life history, alternating seasonally between asexual and sexual protogynous (i.e. sequential) hermaphroditic stages. While predicting future salp bloom frequency and intensity relies on an understanding of the transitions during the sexual stage from female through parturition and subsequent sex change to male, these transitions have not been explored at the molecular level. Here we report the development of the first complete genome of S. thompsoni and the North Atlantic sister species S. aspera. Genome and comparative analyses reveal an abundance of repeats and G-quadruplex (G4) motifs, a highly stable secondary structure, distributed throughout both salp genomes, a feature shared with other tunicates that perform alternating sexual-asexual reproductive strategies. Transcriptional analyses across sexual reproductive stages for S. thompsoni revealed genes associated with male sex differentiation and spermatogenesis are expressed as early as birth and before parturition, inconsistent with previous descriptions of sequential sexual differentiation in salps. Our findings suggest salp are poised for reproductive success at birth, increasing the potential for bloom formation as ocean temperatures rise.</p>
Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics
<p><strong>Background</strong></p> <p><em>Hydrangea petiolaris</em> Siebold & Zucc., also known as climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and Sakhalin Island. It is an economically important ornamental plant with fertile and sterile flowers. Despite the recent increase in <em>Hydrangea</em> breeding and interest in germplasm conservation, relatively little is known about the relationships between <em>Hydrangea</em> species.</p> <p><strong>Results</strong></p> <p>We employed Illumina NovaSeq 6000 sequencing technology to generate a total of 39,945,480 reads, which were assembled into 137,715 contigs. A total of 109,092 filtered transcripts were used to identify microsatellites, and 54,587 microsatellite repeat motifs were revealed within 33,556 contigs. Among these, 4,510 transcripts harboring microsatellites had Gene Ontology annotations, and numerous microsatellite-containing transcripts exhibited associations with genes, including those encoding PPR proteins, aldehyde dehydrogenases, and bHLH transcription factors, related to the <em>restorer of fertility</em> (<em>Rf</em>) genes, which play a critical role in restoring fertility in plants with cytoplasmic male sterility. Validation of transcriptomic SSR markers demonstrated high levels of polymorphism, revealing significant genetic diversity within populations. However, null alleles and deviations from Hardy‒Weinberg equilibrium at specific loci suggested caution in genotyping accuracy. Population-level analysis disclosed high genetic differentiation and distinct clustering of populations.</p> <p><strong>Conclusions</strong></p> <p>The <em>H</em>. <em>petiolaris</em> transcriptomic SSR markers offer valuable insight for gaining insights into the population genetics, evolutionary background, and practical strategies for conserving this species. Moreover, the microsatellite loci we have identified and their associations with annotated genes hold promise for creating functional markers specifically tailored for <em>H</em>. <em>petiolaris</em>. These markers include valuable resources of transcriptomic SSR markers suitable for population genetic investigations and have a reasonable degree of applicability across different taxa.</p>
Projection of high-dimensional genome-wide expression on SOM transcriptome landscapes: supplementary datasets
<p>This is a supplementary dataset with raw data, scripts, and complete analysis results for the paper "Supervised projection of high-dimensional genome-wide expression on SOM transcriptome landscapes". </p> <p>The archive contains three folders:</p> <p>1. "Simdata" folder contains data, scripts, and results of performance evaluation of extension SOM and supervised SOM with simulated data. </p> <p>2. "IBD" - folder contains data, scripts, and results of analysis of Inflammatory bowel disease datasets.</p> <p>3. "BC" - folder contains data, scripts, and results of analysis of breast cancer datasets.</p>
Genomic, transcriptomic and proteomic comparison of MRSA CC398 isolates collected from human and wild animal samples (Genome assembly and annotation dataset)
<p>This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) for the following methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) strains: MRSA CC398 isolates recovered from humans, namely C5621 and C9017, and from a wild boar, namely OR418.</p> <p>All raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB35102).</p>
Hydractinia symbiolongicarpus genome and transcriptome assemblies
<p>Scaffold-level genome assemblies for Hydractinia symbiolongicarpus histoincompatible siblings BC-3 and BC-15 from a back-cross population derived from wildtype individuals . Assemblies generated with ABySS short read assembler using Illumina 200-bp insert paired-end libaries and 3-Kbp insert mate pair 'long jumping distance' libraries. The trimmed read depths were ~36X and ~49X for BC-3 and BC-15, respectively.</p> <p>Transcriptome assemblies for Hydractinia symbiolongicarpus wildtype individuals HWB-103 and HWB-29. Assemblies generated with Trinity using Illumina mRNA libraries.</p>
Figure 2 in Omics in Weed Science: A Perspective from Genomics, Transcriptomics, and Metabolomics Approaches
Figure 2. Workflow of transcript analyses by RNA-Seq and qRT-PCR.
Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
<p>Data and analysis code repository for: </p> <p>Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation</p> <p>https://doi.org/10.1101/255380</p>
Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma
<p>Code and data for manuscript "Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma"</p>
Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)
<p>Intraspecific genetic variation in foundation species such as aspen (<em>Populus</em> <em>tremuloides</em> Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1,243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.</p>
Genome and Transcriptome references based on hg19 from UCSC, 2015
<p>rsem.transcripts.nant2015.fa.gz - bgzipped FASTA reference of transcriptomes</p><p>genome.nant2015.fa.gz - bgzipped FASTA human genome reference, with several viral sequences added.</p><p>refseq.txt.gz - Exact sequence accessions and mapping coordinates for a RefSeq transcriptome based off the UCSC genome browser for hg19.</p><p>Coordinates are BED-style, with one row per transcript, and 1+ transcript per gene.</p><p>Column annotation</p><p>1. RefSeq Accession</p><p>2. Chromosome</p><p>3. Strand</p><p>4. thinStart (gene boundary, including UTR)</p><p>5. thinEnd (gene boundary, including UTR)</p><p>6. thickStart (CDS boundary)</p><p>7. thinStart (CDS boundary)</p><p>8. number of exons</p><p>9. comma separated exon starts</p><p>10. comma separate exon ends</p><p>11. common gene name</p><p>12. refseq gene id</p><p>13. 0 if non-primary transcript, 1 if primary transcript</p>
Data from: "Transcriptome resources for two non-model freshwater crustacean species" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014
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Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
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Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics
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Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)
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Data from: "Transcriptome sequencing of the Antarctic Colobanthus quitensis (Kunth) Bartl (Caryophillaceae)" in Genomic Resources Notes Accepted 1 February 2015 – 31 March 2015
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Chromosome-level assembly of two pearl millet (Cenchrus americanus) genomes, functional annotation and transcriptomes
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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.