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2,556 results for “RNAseq”
Arabidobsis ATR7 2020 RNAseq
<p>Oxidative stress can lead to plant growth retardation, yield loss, and death. The <em>atr7</em> mutant of <em>Arabidopsis thaliana</em> exhibits pronounced tolerance to oxidative stress. Using positional cloning, confirmed by knockout and RNA interference (RNAi) lines, we identified the <em>atr7</em> mutation and revealed that <em>ATR7</em> is a previously uncharacterized gene with orthologs in other seed plants but with no homology to genes in lower plants, fungi or animals. Expression of <em>ATR7</em>-<em>GFP</em> fusion shows that ATR7 is a nuclear-localized protein. RNA-seq analysis reveals that transcript levels of genes encoding abiotic- and oxidative stress-related transcription factors (<em>DREB19, HSFA2, ZAT10</em>), chromatin remodelers (<em>CHR34</em>), and unknown or uncharacterized proteins (<em>AT5G59390, AT1G30170, AT1G21520</em>) are elevated in <em>atr7</em>. This indicates that <em>atr7</em> is primed for an upcoming oxidative stress via pathways involving genes of unknown functions. Collectively, the data reveal <em>ATR7</em> as a novel seed plants-specific nuclear regulator of oxidative stress response.</p>
Methods for Extracting and Characterizing RNA from Urine: for downstream PCR and RNAseq Analysis
<p>Readily accessible samples such as urine or blood are seemingly ideal for differentiating and stratifying patients, however, it has proven a daunting task to identify reliable biomarkers in such samples. Noncoding RNA holds great promise as a source of biomarkers distinguishing physiologic wellbeing or illness.</p>
Single-cell RNAseq of Day 49 midbrain organoids from healthy and alpha-synuclein triplication iPSC lines
<p>Unbiased single-cell RNAseq of Day 49 midbrain dopaminergic organoids (10x 3' v3) of the Patikas et al. publication.</p> <p> </p> <p>The mono-unt-celltypes.h5ad refers to the object shown at Fig 2A and contains 3 cell lines:</p> <ol> <li>KOLF2 ( Control cell line)</li> <li>SNCA-3x alpha Synuclein triplication Parkinson's Disease patient-derived iPSC line</li> <li>SNCA-corr (SNCA-3x isogenic control with the triplication mutation corrected)</li> </ol> <p>The all-celltypes.h5ad refers to the object shown at Fig 4 onwards and contains the 3 cell lines that are included in model-dataset.h5ad and 7 other single-cell RNAseq samples:</p> <ol> <li>SNCA-3x+KOLF2 (chimera organoid condition of SNCA-3x and KOLF2 of iPSCs grown together in a midbrain organoid)</li> <li>SNCA-corr+KOLF2 (chimera organoid condition of SNCA-corr and KOLF2 of iPSCs grown together in a midbrain organoid)</li> <li>5 paired rotenone conditions. For each condition (KOLF2, SNCA-3x, SNCA-corr, SNCA-3x+KOLF2, SNCA-corr+KOLF2) a paired condition with acute 24h rotenone treatment in an antioxidant-free medium.</li> </ol>
Bulk RNAseq of chronic LPS treated female mouse pituitary across doses
<p>To investigate the mechanisms of chronic inflammation on gonadotropin secretion we performed bulk RNA-seq on pituitaries from female mice chronically exposed to lipopolysaccharide for 6 weeks.</p>
Loricarioid catfish evolved skin denticles that recapitulate teeth at the structural, developmental, and genetic levels (raw RNAseq reads)
<p>The first vertebrate mineralized skeleton was an external bony armor coated with dental structures. The subsequent emergence of a mineralized endoskeleton and of teeth are considered key innovations in the diversification of vertebrates. Although time clouds our understanding of the initial evolution of these mineralized structures, recent re-emergences may shed light on the underlying processes. Loricarioid catfishes are a lineage that, much like the ancestral vertebrates, bear denticle-clad bony armor from head to tail. Loricarioid denticles (LDs) and oral teeth are very similar in superstructure. We show here that other extra-oral dental structures are found as ancestral characters only in lineages that are distantly related to loricarioids such as sharks or coelacanth, indicating that LDs have independently re-emerged in loricarioid catfishes. We investigate whether the similarities between LDs and teeth extend to their developmental and genetic context, and how their development compares to that of other vertebrate integument structures. Our detailed study of the development of LDs, and gene expression analyses through in situ hybridization confirm that all 12 genes from the tooth-forming gene regulatory network (oGRN) are expressed in developing LDs in a similar way as they are expressed in developing teeth. We then compare the developmental, structural, and genetic aspects of LD and teeth with that of other integument appendages such as fish scales, shark dermal denticles, feathers and hairs. We find that LDs share all developmental cues with teeth and, to a lesser extent, with the other vertebrate integument structures. Taken together, our results indicate that denticles have re-emerged on the trunk of loricarioid catfishes through the ectopic co-option of the oGRN rather than the resurrection of an ancestral trunk-specific denticle genetic pathway.</p>
RNAseq data of iRECs treated with palmitic acid and oleic acid
<p><span>In diabetic patients, </span><span>dyslipidemia </span><span>frequently contributes to organ damage such as </span><span>diabetic kidney disease (DKD). DKD is associated with excessive renal deposition of triacylglycerol (TAG) in lipid droplets (LD). In order to understand the biological processes ocurring in proximal tubules when exposed to fatty acids</span>, we performed a comparative transcriptomic study on BSA-, BSA-PA-, BSA-OA- and BSA-PA/OA-treated iRECs using RNA sequencing.</p>
RNAseq data and analysis results from hippocampus of IVH+ICP, IVH, and sham control rats
<p>Supporting data from the RNAseq experiments appearing in the original manuscript "Sustained ICP Elevation Is a Driver of Spatial Memory Deficits After Intraventricular Hemorrhage and Leads to Activation of Distinct Microglial Signaling Pathways" accepted to Translational Stroke Research on June 24, 2022 (published July 12, 2022). Full experimental and technical details are available at <a href="https://doi.org/10.1007/s12975-022-01061-0">https://doi.org/10.1007/s12975-022-01061-0</a>. </p>
RNAseq of salivary gland IL10 positive CD4+ Tcells versus IL10 negative CD4+ Tcells at day14 post MCMV infection
<p>Bulk RNAseq, DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) output for salivary gland IL10 positive CD4+ Tcells versus IL10 negative CD4+ Tcells at day14 post MCMV infection.</p>
Liver and Left Ventricle RNAseq data
<p>Raw count files and normalised read count with differential gene expression analysis results files for both liver and left ventricle.</p>
Trimmed RNASeq pair for the Galaxy Training Network tutorial - "Metatranscriptomics analysis using microbiome RNASeq data"
<p>Functional microbiome analysis which estimates the functional groups expressed by microbial community enables researchers to look beyond taxonomic composition and correlation with the condition under study. Using microbial community RNA-Seq data and subsequent metatranscriptomics workflows to elucidate the functional complement of the microbiome is gaining interest in the field. <br> This Galaxy training network tutorial will introduce researchers to the basic concepts and tools from the published ASaiM workflow (Batut et al, <em>GigaScience</em> (2018), 7 (6),<a href="http://dx.doi.org/10.1093/gigascience/giy057"> http://dx.doi.org/10.1093/gigascience/giy057</a>). </p> <p>The dataset is a trimmed version of one of the time points from a cellulose degradation biogas reactor dataset. The dataset has been trimmed to facilitate running the workflows for this tutorial. Any biological interpretation from the results would be incorrect, due to the trimmed version of the dataset.</p>
RnaSeq of Igf2 mRNA injected blastocysts
<p><span>Raw fastq files of Smart-seq3 Sequencing Data of </span>Forty-five parthenotes were injected with Igf2 mRNA (3 ng/µL) plus Gfp mRNA (3 ng/µL) (experimental group) and 45 parthenotes were injected with Gfp mRNA alone (3 ng/µL) (control group).</p> <p> </p>
Data from: Vaginal lactobacilli produce anti-inflammatory beta-carboline (BC) compounds. RNAseq dataset of BC-treated human monocytes.
<p>Primary human monocytes were isolated from peripheral blood mononuclear cells via CD14+ magnetic selection. Monocytes were then treated with 3 beta-carboline compounds isolated from the supernatant of vaginal <em>Lactobacillus crispatus</em> strain MV-1A-US (HM-637). The beta-carbolines are labled 322/BC1; 325/BC3 and 361/BC6. We find that BC6 suppresses inflammatory signaling genes in untreated and in LPS-treated monocytes. FIles include raw reads, count table and code for DESeq2-generated differentially expressed genes. </p>
AD_bulk_RNAseq_review
<p>Supplementary files for the Systematic review and meta-analysis for bulk RNAseq studies comparing brain tissue from Alzheimer's disease patients and controls. </p>
RNASeq fastq files associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This next-generation sequencing 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_RNASeq_FastqFiles</strong>’ contains raw/unprocessed RNASeq Fatsq read files for postnatal day 5 (P5) mouse (Mus) and jerboa (Jac) cartilage samples (Metatarsal = MT; Radius/Ulna = RU).</p> <p>> The <strong>Jac_P5</strong> subfolder contains single-end reads (R1) for five jerboa metatarsals (MT1-5) and radius/ulna (RU1-5) biological replicates. Jac_MT1-3 and Jac_RU1-3 were used in the primary differential expression analysis (n=3). Jac_MT4-5 and Jac_RU4-5 were used for independent validation (n=2) of the the primary analysis. </p> <p>> The <strong>Mus_P5</strong> subfolder contains single-end reads (R1) for five mouse metatarsals (MT1-5) and radius/ulna (RU1-5) biological replicates. Mus_MT1-3 and Mus_RU1,3 & 4 were used in the primary differential expression analysis (n=3). Mus_MT4-5 and Mus_RU4 & 5 were used for independent validation (n=2) of the the primary analysis. </p>
Trinity assembly of thrips RNAseq data -T-ame
<p>De novo Trinity assembly of RNAseq data</p>
Trinity assembly of thrips RNAseq data -THR-E
<p>De novo trinity assembly of thrips NGS RNAseq data</p>
Trinity assembly of thrips RNAseq data -THR-C
<p>De novo trinity assembly of NGS data</p>
single-cell RNAseq data (data set 20) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset20) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from breast cancer samples downloaded from the GEO website (GSE180286)<strong>. </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p> <p> </p>
single-cell RNAseq data (data set 18) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset18) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from Liver cancer set 1 samples downloaded from the GEO website (GSE125449)<strong>. </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p>
single-cell RNAseq data (data set 17) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset17 was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from PBMC metastatic MCC samples downloaded from the GEO website (GSE117988)<strong>. </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p>
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.