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6,617 results for “RNA Sequencing”
RNA sequences for Aedes species, Dengue, and Chikungunya viruses
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Bulk RNA sequencing the zebrafish sox17 lineage at 8, 12, and 24 hours post-fertilization
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RNA sequencing for individuals of Daphnia dentifera exposed and unexposed to a fungal pathogen
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Dataset for: mRNA vaccine quality analysis using RNA sequencing
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Bulk RNA sequencing analysis of Lin- leukemia BCR-ABL and BCR-ABL/MSI2-HOXA9 cells (post-transplantation)
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Global Characterization of Megakaryocytes in Bone Marrow, Peripheral Blood, and Cord Blood by Single-cell RNA Sequencing
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RNA-sequencing dataset of land snails collected in Australia
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Single cell RNA sequencing of human tissue along the stomach-intestinal tract
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Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data - Table S03 - All detected SVs.xlsx
<p>Large concatenated results table on all samples of the Dr. Disco study.</p> <p> </p>
Helicos direct RNA sequencing of FPA mutants and overexpressors
<p>Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat receptor (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, controlling their functional expression and impacting immunity. Using long-read nanopore direct RNA sequencing we resolve the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.</p>
Oxford Nanopore Direct RNA Sequencing datasets for detecting rRNA modifications in the Brassica oleracea mitoribosome
<p>Oxford Nanopore Direct RNA Sequencing (DRS) was applied for the detection of rRNA modifications in the <em>Brassica oleracea</em> mitoribosome. A comparison between native rRNA transcripts and in vitro transcribed (IVT) rRNA transcripts that were devoid of any modification indicated systematic base-calling errors and/or variations in current intensities that led to the prediction of the modified nucleotides (Begik et al., 2018).</p> <p>For Nanopore (DRS) library preparation, custom reverse transcription adapters (RTAs) containing Deeplexicon multiplexing barcodes (BC1, BC2 or BC3) were designed for sequence-specific ligation to the 3’-ends of <em>B. oleracea</em> mitochondrial rRNAs.</p> <p>Basecalling and demultiplexing of ONT direct RNA sequencing data were performed by Guppy and Deeplexicon, respectively.</p> <p>For the analysis and visualization of current intensities, a full description is available in the associated publication.</p> <p>The <strong>Eventalign_18S.R</strong> Rscript was used to make the nanopore <strong>18S </strong>signal analysis</p> <p>The <strong>Eventalign_26S.R</strong> Rscript was used to make the nanopore <strong>26S </strong>signal analysis</p> <p>The raw data for the scripts are in the following folders:</p> <p>- For 26S: 26S_Native.barcode01 and 26S_IVT.barcode03<br>- For 18S: 18S_Native.barcode01 and 18S_IVT.barcode02</p> <p>These folders contain the read alignment files output from minimap2 (in .bam format) and the eventalign files generated by the f5c software (in tsv format).</p> <p>The FASTA folder contains the mitochondrial 18S and 26S rRNA gene reference sequence in fasta format</p>
Integrated single-cell RNA-sequencing data of unwounded and wounded mouse skin and fibroblasts.
<p>This repository contains the .h5ad files that store the integrated scRNA-seq data we generated for the work, Almet et al. (2023), "Fibroblasts evolve in single-cell state to drive extracellular matrix and signaling changes across wound healing", to be published in the Journal of Investigative Dermatology.</p><p>The integrated* files contain both raw counts, normalized counts, as well as unspliced and spliced count estimates that were obtained using kallisto|bustools and velocyto. We integrated the data from the following published datasets:</p><ol><li><a href=" https://doi.org/10.7554/eLife.60066">Phan et al. (2021)</a>: Unwounded P21 mice and small wound P21 + 7 mice</li><li><a href="https://doi.org/10.1016/j.celrep.2020.02.091">Haensel et al. (2020)</a>: Unwounded P49 mice and small wound P49 + 4 mice</li><li><a href="https://doi.org/10.1038/s41467-018-08247-x)">Guerrero-Juarez et al. (2019)</a>: Large wound day 12 mice</li><li><a href="https://doi.org/10.1016/j.stem.2020.07.008">Abbasi et al. (2020)</a>: Large wound day 14 mice</li><li><a href="https://doi.org/10.1126/sciadv.aay3704">Gay et al. (2020)</a>: Large wound fibrotic (hairless) and regenerative (hair follicle neogenesis) day 18 mice</li></ol><p>The unwounded_* files were used to briefly integrated unwounded skin scRNA-seq from mouse models of different ages that have been used to analyze wound healing in <a href="https://doi.org/10.1016/j.celrep.2020.02.091">Haensel et al. (2020),</a> <a href=" https://doi.org/10.7554/eLife.60066">Phan et al. (2021)</a>, and <a href="https://doi.org/10.1016/j.celrep.2022.111155">Vu et al. (2022)</a>, which generated scRNA-seq for unwounded skin from mice aged P21, P49, and P616, respectively. </p><p>The data can be loaded using the Python package Scanpy or AnnData, but you can also load it in R if you use zellkonverter. </p>
RNA sequencing data from the guts of Drosophila wildtype and CG3740/nazo double mutant 20-day-old males
<p>Lipid dyshomeostasis has been implicated in a variety of diseases ranging from obesity to neurodegenerative disorders such as Neurodegeneration with Brain Iron Accumulation (NBIA). Here, we uncover the physiological role of Nazo, the Drosophilamelanogaster homolog of the NBIA-mutated protein – c19orf12, whose function has been elusive. Ablation of Drosophila c19orf12 homologs leads to dysregulation of multiple lipid metabolism genes. nazo mutants exhibit markedly reduced gut lipid droplet and whole-body triglyceride contents. Consequently, they are sensitive to starvation and oxidative stress. Nazo is required for maintaining normal levels of Perilipin-2, an inhibitor of the lipase – Brummer. Concurrent knockdown of Brummer or overexpression of Perilipin-2 rescues the nazo phenotype, suggesting that this defect, at least in part, may arise from diminished Perilipin-2 on lipid droplets leading to aberrant Brummer-mediated lipolysis. Our findings potentially provide novel insights into the role of c19orf12 as a possible link between lipid dyshomeostasis and neurodegeneration, particularly in the context of NBIA.</p>
The 3'-RACE data (InPACT: A computational method for accurate characterization of intronic polyadenylation from RNA sequencing data)
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RNA sequencing code associated with Billipp et al. Immunity 2024 - Chat + vs Chat - tuft cells
<p>R code and result for RNA-sequencing analysis comparing <em>Chat(GFP)+ </em>and <em>Chat(GFP)- </em>tuft cells sorted from the small intestine of <em>B6.Chat-GFP</em> mice. Associated with Billipp et al. Immunity 2024 titled "Tuft cell-derived acetylcholine promotes epithelial chloride secretion and intestinal helminth clearance"</p>
RNA sequencing code associated with Billipp et al. Immunity 2024 - Prox vs. distal tuft cells
<p>R code and result for RNA-sequencing analysis comparing tuft cells sorted from the proximal and distal small intestine of mice. Associated with Billipp et al. Immunity 2024 titled "<span>Tuft cell-derived acetylcholine promotes epithelial chloride secretion and intestinal helminth clearance</span>"</p>
Single nucleus RNA-sequencing data related to Van Hijfte et al. 2024
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RNA sequencing data from the prefrontal cortex and hippocampus of male (12 weeks old) hemizyguous CAG-HERV-W-env mice and wild-type controls
<p>RNA sequencing data from the prefrontal cortex (PFC) and hippocampus (HIPP) of male (12 weeks old) hemizyguous CAG<sup>HERV-Wenv </sup>mice ( C57BL6/J;129P2/Ola-Hprt mice; <em>n</em> = 3) relative to wild-type ( <em>n</em> = 3) littermates. Total RNA was extracted from prefrontal and hippocampal samples using the SPLIT RNA extraction kit (Lexogen, Austria) following the manufacturer’s recommendations and was sent to the Functional Genomics Center in Zurich (FGCZ) for quality control and RNA sequencing. The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1, a 28S/18S ratio within 1.5–2, and RIN (>8) values qualified for a Poly-A enrichment strategy in order to generate the sequencing libraries applying the TruSeq mRNA Stranded Library Prep Kit (Illumina, Inc, California, USA). After Poly-A selection using Oligo-dT beads the mRNA was reverse-transcribed into cDNA. The cDNA was fragmented, end-repaired and poly-adenylated before ligation of TruSeq UD Indices (IDT, Coralville, Iowa, USA). The quality and quantity of the amplified sequencing libraries were validated using a Fragment Analyzer SS NGS Fragment Kit (1–6000 bp) (Agilent, Waldbronn, Germany). The equimolar pool of the samples was spiked into a NovaSeq6000 run targeting ~15M reads per sample on a S1 FlowCell (Novaseq S1 Reagent Kit, 100 cycles, Illumina, Inc, California, USA). Reads were quality-checked with FastQC. Sequencing adapters were removed with Trimmomatic and aligned to the reference genome and transcriptome of Mus Musculus (GENCODE, GRCm38,p5) with STAR v2.7.3. Distribution of the reads across genomic isoform expression was quantified using the R package GenomicRanges from Bioconductor Version 3.10. Minimum mapping quality, as well as minimum feature overlaps, was set to 10. Multi-overlaps were allowed. Differentially expressed genes (DEGs) were identified using the R package edgeR from Bioconductor Version 3.10, using a generalized linear model (glm) regression, a quasi-likelihood (QL) differential expression test and the trimmed means of M-values (TMM) normalization.</p>
Whole animal single nuclei RNA sequencing data of catenulid Stenostomum brevipharyngium
<p>Provided is the count tables as well as the final h5ad. </p>
Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of Ms4a3Ai14, BM chimeric mice (CD45.2 Csf2rb-/-: CD45.1 Csf2rb+/+ and CD45.2 Ifngr1-/-: CD45.1 Ifngr1+/+) using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.
<p><strong>Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of <em>Ms4a3</em><sup>Ai14</sup> at onset and peak EAE, BM chimeric mice (CD45.2 <em>Csf2rb</em><sup>-/-</sup>: CD45.1 <em>Csf2rb</em><sup>+/+</sup> and CD45.2 <em>Ifngr1<sup>-/-</sup></em>: CD45.1 <em>Ifngr1<sup>+/+</sup></em>) using 10X Genomics platform.</strong></p> <p>The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.</p> <p>Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from <em>Ms4a3</em><sup>Ai14</sup> mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.</p>
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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.