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8 results for “IGV”
Schistosoma mansoni ATAC-seq results for IGV (female and male worms with and without LSD1 inhibitor)
<p>In this study, the anti-schistosomal activity of 39 <em>Homo sapiens</em> Lysine Specific Demethylase 1 (HsLSD1) inhibitors was investigated on parasitic life cycle stages associated with both definitive and intermediate host infection. Amongst this collection of small molecules, compound <strong>33</strong> was the most potent and reduced <em>ex vivo</em> viabilities of schistosomula, juveniles, miracidia and adults. At its sub-lethal concentration to adults (3.13 µM), compound <strong>33 </strong>also significantly impacted oviposition, ovarian as well as vitellarian architecture and gonadal/neoblast stem cell proliferation. ATAC-seq analysis of adults demonstrated that compound <strong>33</strong> significantly affected chromatin structure (intragenic regions > intergenic regions), especially in genes differentially expressed in cell populations (e.g., germinal stem cells, hes2<em><sup>+</sup></em>stem cell progeny, S1 cells and late female germinal cells) linked to these <em>ex vivo</em> phenotypes.</p> <p>The data presented here allow for visualisation in IGV https://igv.org/app/</p> <p>Produced in collaboration with IHPE. </p>
IGV Bundle for Rhizophagus irregularis DAOM-197198
<p>Use these files to build your own genome browser for the "Rhiir3" <em>Rhizophagus irregularis</em> DAOM-197198 chromosome-scale genome assembly (PRJNA885267). Tracks available:</p> <p><strong>Gene annotation, based on Illumina and Nanopore RNA-Seq reads. </strong><br> Gene models were curated by excluding genes with InterPro domains related to transposable elements.<br> File: Rhiir3_PRJNA885267_genes.gff3</p> <p><strong>Repeat annotation. </strong><br> The repeat library was made using EDTA (Ou et al., 2019), and curated by excluding consensus sequences with InterPro domains of known cellular genes. Repeats were then masked using RepeatMasker (parameters -s -no_is -norna -nolow -div 40) (Smit et al., 2015). Unclassified repeats are grey-coloured and repeats classified into transposable elements categories are colour-coded: LINEs are blue, DNA transposons are pink and LTRs are green.<br> File: Rhiir3_PRJNA885267_repeats.gff3</p> <p><strong>Highly methylated CG sites, called via direct Nanopore genomic DNA sequencing of <em>R. irregularis </em>spores.<em> </em></strong><br> 161Gb of raw FAST5 files obtained from three R9.4.1 Nanopore flow cells were basecalled with Guppy5, producing 985,449 reads which were successfully processed by tombo (Stoiber et al., 2017) and used by DeepSignal2 (Ni et al., 2019) to extract CG motifs and to call 5mC modifications using a human model (model.dp2.CG.R9.4_1D.human_hx1.bn17_sn16.both_bilstm.b17_s16_epoch4.ckpt. Only CG sites with >80% 5mC are shown, and the track indicates methylation ratios measured as a fraction of 1 (0.80 to 1.00).<br> File: Rhiir3_PRJNA885267_high_meth_CG.bed</p> <p><strong>Index for CG methylation sites.</strong><br> File: Rhiir3_PRJNA885267_high_meth_CG.bed.idx</p> <p><strong>Nanopore RNA-Sequencing reads, poly(A)+ cDNA-PCR, from <em>R. irregularis</em> spores. </strong><br> Reads were trimmed of adapters and cleaned with seqclean to remove a percentage of undetermined bases, polyA tails, overall low complexity sequences and short terminal matches. Cleaned sequences were then mapped using minimap2 (options: -G max intron length=3000, -ax, map-ont).<br> File: Rhiir3_PRJNA885267_nano_cDNA.bam</p> <p><strong>Index for Nanopore RNA-Sequencing reads.</strong><br> File: Rhiir3_PRJNA885267_nano_cDNA.bam.bai</p> <p><strong>Small RNA loci.</strong><br> 70,956,710 small RNA-Seq reads from two replicates of oxidised and two replicates of column-purified spore RNA (Dallaire et al., 2021) were used to run ShortStack (Axtell, 2013) (parameters --dicermin 20 --dicermax 27 --foldsize 300 --pad 200 --mincov 10.0rpm --strand_cutoff 0.8 --mmap r).<br> File: Rhiir3_PRJNA885267_small_RNA_loci.gff3</p> <p><strong>Small RNA sequencing reads.</strong><br> Shortstack small RNA-Seq alignments, with multi-mappers randomly distributed.<br> File: Rhiir3_PRJNA885267_small_RNA.bam<br> <br> <strong>Index for small RNA sequencing reads.</strong><br> File: Rhiir3_PRJNA885267_small_RNA.bam.bai</p>
Raw data of RNA-seq and IGV -2
<p>Raw data of RNA-seq and IGV of infected samples and mock infected samples</p>
EUS-guided Combined Therapy Versus Beta Blocker Therapy in Primary Prophylaxis o GOV II and IGV I
ClinicalTrials.gov study NCT04075760. IPD Sharing: NO. Countries: 1. Publications: 1.
IGV-results of Bowtie mapping
<p> Visualize sequence read alignment data.</p>
IGV screenshot for manual validation of 60 reported false positive small CNVs in SurVIndel2
Open the record for dataset details and reuse information.
Raw data of RNA-seq and IGV -1
<p>The raw data of RNA-seq and IGV data of infected samples and bacterial samples.</p>
Supplementary IGV data for Human Embryonic RNA Editome
<p>Supplementary IGV data for Human Embryonic RNA Editome</p>
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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.