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Dataset results
7 results for “Nanopore, direct RNA sequencing, RNA modifications”
xPore: Identification of differential RNA modifications from nanopore direct RNA sequencing
<p>xPore is a Python package for identification and quantification of differential RNA modifications from direct RNA sequencing.</p> <p>The detailed usage is documented at <a href="https://xpore.readthedocs.io/en/latest/">https://xpore.readthedocs.io/en/latest</a>, while all scripts and source code are available at <a href="https://github.com/GoekeLab/xpore">https://github.com/GoekeLab/xpore</a>.</p> <p>All the preprocessed datasets used in the paper are provided here. </p> <p>Please cite our paper below when using these data.<br> Ploy N. Pratanwanich et al. "Detection of differential RNA modifications from direct RNA sequencing of human cell lines." bioRxiv (2020).</p>
xPore: Identification of differential RNA modifications from nanopore direct RNA sequencing - SGNEx data
<p>xPore is a Python package for identification and quantification of differential RNA modifications from direct RNA sequencing.</p> <p>The detailed usage is documented at <a href="https://xpore.readthedocs.io/en/latest/">https://xpore.readthedocs.io/en/latest</a>, while all scripts and source code are available at <a href="https://github.com/GoekeLab/xpore">https://github.com/GoekeLab/xpore</a>.</p> <p>All the preprocessed datasets used in the paper are provided here. </p> <p>Please cite our paper below when using these data.<br> Ploy N. Pratanwanich et al. "Detection of differential RNA modifications from direct RNA sequencing of human cell lines." bioRxiv (2020).</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>
Simultaneous profiling of ac4C and m5C modifications from nanopore direct RNA sequencing
GEO Series GSE267558. Oryza sativa. 1 samples. Type: Expression profiling by high throughput sequencing.
Detection of SINEUP RNA modification by Oxford Nanopore direct-RNA sequencing
GEO Series GSE224018. Homo sapiens. 3 samples. Type: Other.
Transfer learning enables identification of multiple types of RNA modification using nanopore direct RNA sequencing
GEO Series GSE227087. Oryza sativa; synthetic construct. 8 samples. Type: Expression profiling by high throughput sequencing.
The detecting of m6A RNA modifications upon Oxford Nanopore direct-RNA sequencing [Nanopore]
GEO Series GSE290245. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.