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25,372 results for “Transcriptomics”
Spatial transcriptomics images for papillary and anaplastic thyroid cancer IRIBHM dataset
<p>This dataset includes the image files for spatial transcriptomics data associated with the publication "Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers".</p>
Transcriptome of Peromyscus leucopus lungs infected with SARS-CoV-2
<p><em>Peromyscus leucopus</em> is a reservoir for numerous zoonoses and one of the most abundant mammals in North America. Since they live near humans we are interested in the possibility of SARS-CoV-2 infection in this animal model from a zoonoses standpoint. The experimental design for the first trial involves using adult male and female <em>P. leucopus</em> LL stock. Animals were dosed with nasal inhalation of either tissue culture medium (DMEM) alone (controls) or alpha variant, WA1 strain of SARS-CoV-2 virus. We dosed 8 animals with a virus (titer 2x104) and 6 with DMEM alone. Animals were euthanized at either 3 or 6 days post-infection. For a second trial, <em>P. leucopus</em> animals were 1-3 years old and we had 3 groups: control animals with nasal inhalation of media, control animals with nasal inhalation of the heat-treated virus, and infected animals. Each group has 4 animals euthanized on 3- or 6-days post-infection (DPI). Lung tissue was used for RNA isolation and further sequencing to obtain 40 x 106 PE150 reads.</p>
CosMx Spatial transcriptome dataset of human gastric mucosa
<p>This dataset contains the spatial transcriptome dataset of human gastric mucosa obtained by CosMx</p> <p>A zip file contains the following folders and files:</p> <p><strong>Folders</strong></p> <p>- CellComposite folder: the composite immunofluorescent images of each FOV.</p> <p>- CellLabels folder: the cell definitions images for each FOV determined during cell segmentation.</p> <p>- CellOverlay folder: the cell boundary images for each FOV determined during cell segmentation.</p> <p>- CompartmentLabels folder: the subcellular compartment images for each FOV determined during cell segmentation. The compartment types are as follows: 0. Extracellular, 1. Nuclear, 2. Membrane, 3. Cytoplasmic</p> <p>- RawMorphologyImages folder: raw morphological TIF images for each FOV</p> <p> </p> <p><strong>Files</strong></p> <p>- Run5458_{sample_name}_exprMat_file.csv: cell expression matrix.</p> <p>- Run5458_{sample_name}_fov_positions_file.csv: each FOV relative position within global structure.</p> <p>- Run5458_{sample_name}_metadata_file.csv: the metadata of each cell.</p> <p>- Run5458_{sample_name}_tx_file.csv: the transcript file for each target gene and its position.</p> <p>- Run5458_{sample_name}-polygons.csv: the segmentation polygon file.</p> <p> </p> <p><strong>Citation</strong></p> <p>If you use this dataset for your research, please cite our paper.</p> <p>Ayumu Tsubosaka, Daisuke Komura, Miwako Kakiuchi, Hiroto Katoh, Takumi Onoyama, Asami Yamamoto, Hiroyuki Abe, Yasuyuki Seto, Tetsuo Ushiku, Shumpei Ishikawa, Stomach encyclopedia: Combined single-cell and spatial transcriptomics reveal cell diversity and homeostatic regulation of human stomach, Cell Reports, Volume 42, Issue 10, 2023, 113236, https://doi.org/10.1016/j.celrep.2023.113236.</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: Human conjunctival transcriptome in Acanthamoeba keratitis: An exploratory study
<p>The host conjunctival transcriptome of 9 patients with <em>Acanthamoeba</em> keratitis (AK) is compared to the conjunctival transcriptome of 13 patients with keratitis and no identified pathogen. Pathway enrichment analysis identified thirty-six transcripts as most differentially expressed between patients with AK compared to patients with presumed sterile keratitis.</p>
Ocular Pathogen and Transcriptome Investigation Using Comprehensive Sequencing
ClinicalTrials.gov study NCT05286203. IPD Sharing: NO. Countries: 1. Publications: 1.
Flura-seq for Evaluating the Effects of Different Hyperthermic Intraperitoneal Chemotherapy Regimens on the Transcriptome of Pseudomyxoma Peritonei
ClinicalTrials.gov study NCT06839378. IPD Sharing: YES. Countries: 1. Publications: 9.
The Impact of Imprinting and Repeated Influenza Vaccination on Adaptive Immunity, Transcriptomics, and Metabolomics
ClinicalTrials.gov study NCT03686514. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem
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Dataset for the transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory
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zigzag: A Hierarchical Bayesian Mixture Model for Inferring the Expression State of Genes in Transcriptomes
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Data from: Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)
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Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence
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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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Foraging behaviour variations, for gene expression and transcriptomic divergence in parasitic wasp populations of Venturia canescens
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Single-cell spatial transcriptomics of an inducible destabilized-domain Cre mouse line to target disease associated microglia
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Acute effects on the human peripheral blood transcriptome of decompression sickness secondary to scuba diving: Supplementary datasets
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Morphological and transcriptomic responses/acclimations of erect-type submerged macrophyte Hydrilla verticillata both at low-light exposure and light recovery phases
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Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoa Willd.) in response to photoperiod and plant development
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Transcriptome of Peromyscus leucopus lungs infected with SARS-CoV-2
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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)
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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.