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699 results for “association transcriptomics”
Data from: Comparative transcriptomics reveals domestication-associated features of Atlantic salmon lipid metabolism
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Data from: Transcriptome-derived tetranucleotide microsatellites and their associated genes from the giant panda (Ailuropoda melanoleuca)
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Fat distribution in women associates with depot-specific transcriptomics signatures and chromatin structure
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Transcript expression data. Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes
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Transcriptome-wide comparisons and virulence gene polymorphisms of host-associated genotypes of the cnidarian parasite Ceratonova shasta in salmonids
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BRCA1- and BRCA2- mutation associated transcriptome landscapes in breast and ovarian cancers: ml-SOM results
<p>This is the submission accompanying raw result files for multiple-layer SOM (ml-SOM) analysis for the paper "Transcriptome patterns of BRCA1- and BRCA2- mutated breast and ovarian cancers".</p> <p>The dataset contains the results of the ml-SOM analysis of RNA-sequencing data from TCGA-OV (ovarian cancer) and TCGA-BRCA (breast cancer) projects. </p> <p>The dataset is organized as follows:</p> <ul> <li>Folder <strong>"12.BC.40 - Results" </strong>- ml-SOM analysis of TCGA-BRCA (breast cancer) dataset</li> <li>Folder <strong>"12.OV.40 - Results"</strong> - ml-SOM analysis of TCGA-OV (ovarian cancer) dataset</li> <li>File <strong>"12.BC.40.RData"</strong> - R data file that contains ml-SOM environment for breast cancer</li> <li>File <strong>"12.OV.40.RData"</strong> - R data file that contains ml-SOM environment for breast cancer</li> </ul> <p>For detailed instructions on browsing the results and their interpretation please refer to the oposSOM package manual [1], as well as original publications [2-4]. </p> <p><strong>References</strong></p> <ol> <li>Henry Loeffler-Wirth, Hoang Thanh Le and Martin Kalcheropos. SOM.Comprehensive analysis of transcriptome data. DOI: <a href="https://doi.org/doi:10.18129/B9.bioc.oposSOM">10.18129/B9.bioc.oposSOM</a> </li> <li>Löffler-Wirth H, Kalcher M, Binder H. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on Bioconductor. Bioinformatics. 2015 Oct 1;31(19):3225-7. DOI: 10.1093/bioinformatics/btv342. Epub 2015 Jun 10.</li> <li>Wirth H, von Bergen M, Binder H. Mining SOM expression portraits: feature selection and integrating concepts of molecular function. BioData Min. 2012 Oct 8;5(1):18. DOI: 10.1186/1756-0381-5-18.</li> <li>Wirth H, Löffler M, von Bergen M, Binder H. Expression cartography of human tissues using self-organizing maps. BMC Bioinformatics. 2011 Jul 27;12:306. DOI: 10.1186/1471-2105-12-306.</li> </ol>
Supplemental material from: ESR1 mutations associated with EIS change conformation of ligand receptor complex and alter transcriptome profile
Estrogen insensitivity syndrome (EIS) arises from rare mutations in estrogen receptor α (ERα, encoded by ESR1 gene) resulting in the inability of estrogen to exert its biological effects. Due to the rarity, mutations in ESR1 gene and the underlying molecular mechanisms of EIS have not been thoroughly studied. Here, we investigate known ESR1 mutants, Q375H and R394H, associated with EIS patients using in vitro and in vivo systems. Comparison of the transcriptome and DNA methylome from stable cell lines of both Q375H and R394H clinical mutants show a differential profile compared to WT ERα resulting in loss of estrogen-responsiveness. Molecular dynamic simulation shows that both ESR1 mutations change the ERα conformation of the ligand receptor complexes. Furthermore, we generated a mouse model Esr1-Q, harboring the human mutation using CRISPR/Cas9 genome editing. Female and male Esr1-Q mice are infertile and have similar phenotypes to αERKO mice. Overall phenotypes of the Esr1-Q mice correspond to those observed in the Q375H patient. Finally, we explore the effects of a synthetic progestogen and a GnRH inhibitor in the Esr1-Q mice for potentially reversing the impaired female reproductive tract function. These findings provide an important basis for understanding the molecular mechanistic consequences associated with EIS.
Immuno-transcriptomic profiling of blood and tumor tissue identifies gene signatures associated with immunotherapy response in metastatic bladder cancer
<p>The dataset contains RNA-sequencing data (raw fastq files, not trimmed) of whole blood and whole bladder tissue samples and metadata file with sample annotation. The samples have been collected in the context of the study "Immuno-transcriptomic profiling of blood and tumor tissue identifies gene signatures associated with immunotherapy response in metastatic bladder cancer". In this study, we investigated which are the local and systemic immune changes in an experimental model of muscle-invasive bladder cancer upon immunotherapy. The RNA-sequencing data have been used to produce the results presented in the study. Please refer to the study publication material and methods and the metadata file for details.</p>
Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison
<p>Petal size determines the value of ornamental plants, and thus their economic worth. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes regulating petal size in rapeseed (<i>Brassica napus</i>), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 17 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with extreme differences in petal size identified 11 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, <i>BnaA05</i><i>.</i><i>RAP2.2</i> homologous to <i>RAP2.2</i> in rapeseed may be a critical gene negatively influencing petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two extreme accessions were determined mainly by cell number differences. Finally, we propose a preliminary model for the control of petal size in rapeseed. Our results provide insights into the genetic mechanisms regulating petal size, and also lay the foundation for a better understanding of petal development in plants.</p>
Supplementary material 1 from: Felden A, Paris C, Chapple DG, Suarez AV, Tsutsui ND, Lester PJ, Gruber MAM (2019) Native and introduced Argentine ant populations are characterised by distinct transcriptomic signatures associated with behaviour and immunity. NeoBiota 49: 105-126. https://doi.org/10.3897/neobiota.49.36086
: Data type: molecular data
Analysis code and additional data associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The folder ‘<strong>Zenodo_Saxena_etal_2021_AdditionalData_AnalysisCode</strong>’ contains:</p> <p>> Analysis code used for jerboas-mouse differential RNASeq analysis (<strong>saxena_Interspecies_DESEQ2_analysis.R</strong>).</p> <p>> A folder <strong>Mus_Jac_gtfDir</strong> with two gtf annotation files for 1:1 orthologs in Mouse (musAnno4_1To1Orthologs) and Jerboa (jerboaAnno4_1To1Orthologs) genomes generated with CESAR. This folder also contains two files with mouse or jerboa gene lengths in non-overlapping exons of each gene in the 1:1 orthologous GTF annotations (suffixed "*_exon_lengths_per_gene.txt"). A supporting R library required to run the analysis is provided in this folder (saxena_shared_library_v2.R).</p> <p>>A <strong>STAR_countsDir</strong> folder with STAR generated GeneCounts for mouse and jerboa samples (suffixed "*_SR50"). Subfolders contain metatarsal (MT) and Radius/ulna (RU) STAR Genecounts used in the primary (“*_n=3") and independent validation ("*_n=2") analyses.</p> <p>> A pdf file with <strong>Additional Figures 1 and 2</strong>. Fig 1 shows RNAScope <em>in situs </em>for <em>Galnt17</em> in jerboa and mouse postnatal day 5 cartilages. Fig 2 shows DESeq2 generated MA-plot for jerboa-mouse metatarsal comparisons (n=3).</p> <p>> <strong>Additional Data Tables_1to3</strong> with DESeq2 differential expression results for all of the 17,464 mouse and jerboa orthologs in the primary (n=3, Table1) and independent validation (n=2, Table2) analyses. r-log transformed gene counts for 17,464 mouse and jerboa 1:1 orthologs in metatarsal samples (n=3, Table3).</p>
Tomopteris sp. Transcriptome data and associated annotations
<p>Transcriptome sequences for specimen RAD2-051, Tompteris sp. </p> <p>Files are:</p> <p>RAD2-051_ISOseq_clustered.hq.fasta --> Long read PacBio IsoSeq assembly of Tomopteris mRNA, from body segments</p> <p>RAD2-051_combinedAssembly_c0.95_EXPRfilt_nocontam.fasta --> Combined Trinity and IsoSeq assemblies to capture all expressed genes in dorsal cirri and body segments. Contaminants removed by expression count level filtering and manual removal of human, drosophila, and xenopus sequences (100% blastn hits).</p> <p>RAD2-051_combinedAssembly_c0.95_EXPRfilt_nocontam.fasta.transdecoder.pep --> translated proteins from the combined assembly file.</p> <p>RAD2-051.tsv --> InterProScan annotation for RAD2-051 proteins.</p> <p>RAD2-051.x.swissprot.BLASTXOUT-hssp.txt --> best BLASTX hits of RAD2-051 transcripts against the curated SwissProt database.</p> <p>RAD2-051_Tomopteris.sp.counts.CPMs.csv --> file with read counts in CPMs for mRNA quantification for samples from dorsal cirri and body segments. LA=Left antenna (dorsal cirrus); RA=Right antenna (dorsa cirrus); BD=body segment sample.</p> <p>RAD2-051.iproscan.goa --> a gene ontology annotation file for RAD2-051 annotations from interproscan. For use with topGO in R.</p> <p> </p> <p> </p> <p> </p> <p> </p>
Time-course adaptive changes in hippocampal transcriptome and synaptic function induced by simulated microgravity associated with cognition
<p>Introduction: The investigation of cognitive function in microgravity, both short-term and long-term, remains largely descriptive. And the underlying mechanisms of the changes over time remain unclear. Methods: Behavioral tests, electrophysiological recording, and RNA sequencing were used to observe differences in behavior, synaptic plasticity, and gene expression. Results: Initially, we measured the performance of spatial cognition exposed to long-term simulated microgravity (SM). Both working memory and advanced cognitive abilities were enhanced. Somewhat surprisingly, the synaptic plasticity of the hippocampal CA3-CA1 synapse was impaired. To gain insight into the mechanism of changing regularity over time, transcriptome sequencing in the hippocampus was performed. The analysis identified 20 differentially expressed genes (DEGs) in the hippocampus after short-term modeling, 19 of which were up-regulated. Gene ontology (GO) analysis showed that these up-regulated genes were mainly enriched in synaptic-related processes, such as <em>Stxbp5l</em> and <em>Epha6</em>. This might be related to the enhancement of working memory performance under short-term SM exposure. Under exposure to long-term SM, 7 DEGs were identified in the hippocampus, all of which were up-regulated and related to oxidative stress and metabolism, such as <em>Depp1</em> and <em>Lrg1</em>. Compensatory effects occurred with increased modeling time. Discussion: To sum up, our current research indicates that the cognitive function under SM exposure is consistently maintained or potentially even being enhanced over both short and long durations. The underlying mechanisms are intricate and potentially linked to the differential expression of hippocampal-associated genes and alterations in synaptic function, with these effects being time-dependent. The present study will lay the experimental and theoretical foundation of the multi-level mechanism of cognitive function under space flight.</p>
Transcriptomal and Molecular Characterization of Tumor Associated Monocytes/Macrophages in Human Cancers
ClinicalTrials.gov study NCT00979277. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Transcriptome analyses reveal genes and pathways associated with fatty acid composition traits in pigs
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Data from: De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism
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Data from: The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc, and its association with wing shape in Drosophila melanogaster
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Data from: Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers
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Supplemental material from: ESR1 mutations associated with EIS change conformation of ligand receptor complex and alter transcriptome profile
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Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison
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ScienceDex guides
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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.