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long read rna-sequencing data  (Oxford Nanopore)

 
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    Oxford Nanopore long read rna-sequencing data
    Long Read Rna Sequencing Data, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/sequencing+data+long+read/rna+sequencing/pmc11387194__41588_2024_1872_MOESM1_ESM-266-0-0
    Average 90 stars, based on 1 article reviews
    long read rna-sequencing data - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Sequencing:

    Article Title: Pooled, long-read sequencing for structural variant characterization in schistosome populations.
    Article Snippet: .. 30 31 Results 32 Sequencing Results – We generated long read data with Oxford Nanopore Technologies (ONT) 33 sequencing platform for five lab populations of S. mansoni; SmBRE, SmEG, SmOR and two 34 AC CE P ED M AN US CR IP T Downloaded from https://academ ic.oup.com /gbe/advance-article/doi/10.1093/gbe/evaf127/8176509 by guest on 28 June 2025 populations recently selected from a single population SmLE-PZQ-ER and SmLE-PZQ-ES (Table 1 1). ..

    Article Title: Intra-Strain Genetic Heterogeneity in Toxoplasma gondii ME49: Oxford Nanopore Long-Read Sequencing Reveals Copy Number Variation in the ROP8-ROP2A Locus
    Article Snippet: We selected three ME49 T. gondii isolates for characterization: 2015T, obtained from ATCC (catalog number 50611) thawed in 2015, expanded for two passages, refrozen and then continuously propagated in cell culture from 2022 onward; 2020T, obtained in 2020 from ATCC (catalog number 50611) and propagated in cell culture; and 2000B, originally obtained in the early 1990s and propagated in CD1 mice ( ; see Supplementary Note for additional details on the propagation history of these isolates). .. We generated single-molecule long-read Oxford Nanopore R10 sequencing data for the three isolates , yielding 203X genomic coverage at a read N50 of 37kb for isolate 2015T; 20X genomic coverage at a read N50 of 5kb for isolate 2020T; and 23X genomic coverage at a read N50 of 12.8kb for isolate 2000B. ..

    Article Title: The mitochondrial methylation potential gates mitoribosome assembly.
    Article Snippet: All mass spectrometry proteomics datasets are deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD055907 (SILAC gradient proteomics), PXD062614 (Skeletal muscle proteomics) and PXD019550 [http://proteomecentral.proteomexchange.org/cgi/ GetDataset?ID=019550] (MEF proteomics). .. Direct long-read Oxford Nanopore RNA sequencing raw data have been deposited to NCBI Sequence Read Archive (SRA) with the BioProject accession number: PRJNA1192297. .. Atomicmodels and cryo-EMmapshave beendeposited to Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB)with the following IDs: 9HCC and EMD-52044 (State A1); 9HCD and EMD-52045 (state A2); 9HCE and EMD-52046) (state A3); EMD52408 (state A4); 9E9C and EMD-47791 (state B1); 9HCF; EMD-52047 (state B2); EMD-52430 (state C1); 9HCH and EMD-52049 (state C2) and 9HCG and EMD-52048 (state D).

    Article Title: The mitochondrial methylation potential gates mitoribosome assembly
    Article Snippet: All mass spectrometry proteomics datasets are deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD055907 (SILAC gradient proteomics), PXD062614 (Skeletal muscle proteomics) and PXD019550 [ http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=019550 ] (MEF proteomics). .. Direct long-read Oxford Nanopore RNA sequencing raw data have been deposited to NCBI Sequence Read Archive (SRA) with the BioProject accession number: PRJNA1192297 . .. Atomic models and cryo-EM maps have been deposited to Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) with the following IDs: 9HCC and EMD-52044 (State A1); 9HCD and EMD-52045 (state A2); 9HCE and EMD-52046 ) (state A3); EMD-52408 (state A4); 9E9C and EMD-47791 (state B1); 9HCF ; EMD-52047 (state B2); EMD-52430 (state C1); 9HCH and EMD-52049 (state C2) and 9HCG and EMD-52048 (state D).

    Article Title: Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis.
    Article Snippet: .. Price, R. J. et al. Chromosome-scale genome sequence assemblies of the ‘Autumn Bliss’ and ‘Malling Jewel’ cultivars of the highly heterozygous red raspberry Rubus idaeus L.) derived from long-read Oxford Nanopore sequence data. ..

    Generated:

    Article Title: Pooled, long-read sequencing for structural variant characterization in schistosome populations.
    Article Snippet: .. 30 31 Results 32 Sequencing Results – We generated long read data with Oxford Nanopore Technologies (ONT) 33 sequencing platform for five lab populations of S. mansoni; SmBRE, SmEG, SmOR and two 34 AC CE P ED M AN US CR IP T Downloaded from https://academ ic.oup.com /gbe/advance-article/doi/10.1093/gbe/evaf127/8176509 by guest on 28 June 2025 populations recently selected from a single population SmLE-PZQ-ER and SmLE-PZQ-ES (Table 1 1). ..

    Article Title: Intra-Strain Genetic Heterogeneity in Toxoplasma gondii ME49: Oxford Nanopore Long-Read Sequencing Reveals Copy Number Variation in the ROP8-ROP2A Locus
    Article Snippet: We selected three ME49 T. gondii isolates for characterization: 2015T, obtained from ATCC (catalog number 50611) thawed in 2015, expanded for two passages, refrozen and then continuously propagated in cell culture from 2022 onward; 2020T, obtained in 2020 from ATCC (catalog number 50611) and propagated in cell culture; and 2000B, originally obtained in the early 1990s and propagated in CD1 mice ( ; see Supplementary Note for additional details on the propagation history of these isolates). .. We generated single-molecule long-read Oxford Nanopore R10 sequencing data for the three isolates , yielding 203X genomic coverage at a read N50 of 37kb for isolate 2015T; 20X genomic coverage at a read N50 of 5kb for isolate 2020T; and 23X genomic coverage at a read N50 of 12.8kb for isolate 2000B. ..

    RNA Sequencing:

    Article Title: The mitochondrial methylation potential gates mitoribosome assembly.
    Article Snippet: All mass spectrometry proteomics datasets are deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD055907 (SILAC gradient proteomics), PXD062614 (Skeletal muscle proteomics) and PXD019550 [http://proteomecentral.proteomexchange.org/cgi/ GetDataset?ID=019550] (MEF proteomics). .. Direct long-read Oxford Nanopore RNA sequencing raw data have been deposited to NCBI Sequence Read Archive (SRA) with the BioProject accession number: PRJNA1192297. .. Atomicmodels and cryo-EMmapshave beendeposited to Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB)with the following IDs: 9HCC and EMD-52044 (State A1); 9HCD and EMD-52045 (state A2); 9HCE and EMD-52046) (state A3); EMD52408 (state A4); 9E9C and EMD-47791 (state B1); 9HCF; EMD-52047 (state B2); EMD-52430 (state C1); 9HCH and EMD-52049 (state C2) and 9HCG and EMD-52048 (state D).

    Article Title: The mitochondrial methylation potential gates mitoribosome assembly
    Article Snippet: All mass spectrometry proteomics datasets are deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD055907 (SILAC gradient proteomics), PXD062614 (Skeletal muscle proteomics) and PXD019550 [ http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=019550 ] (MEF proteomics). .. Direct long-read Oxford Nanopore RNA sequencing raw data have been deposited to NCBI Sequence Read Archive (SRA) with the BioProject accession number: PRJNA1192297 . .. Atomic models and cryo-EM maps have been deposited to Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) with the following IDs: 9HCC and EMD-52044 (State A1); 9HCD and EMD-52045 (state A2); 9HCE and EMD-52046 ) (state A3); EMD-52408 (state A4); 9E9C and EMD-47791 (state B1); 9HCF ; EMD-52047 (state B2); EMD-52430 (state C1); 9HCH and EMD-52049 (state C2) and 9HCG and EMD-52048 (state D).

    Article Title: The mitochondrial methylation potential gates mitoribosome assembly.
    Article Snippet: .. The direct long-read Oxford Nanopore RNA sequencing raw data have been uploaded to NCBI SRA database with the BioProject accession number: PRJNA1192297. ..

    other:

    Article Title: Inducible formation of fusion transcripts upregulates haploinsufficient CHD2 gene expression
    Article Snippet: Long read RNA-seq data generated by Oxford Nanopore sequencing was downloaded from the ENA database project PRJEB44348, and mapped to the hg38 human genome assembly using minimap2 .

    Derivative Assay:

    Article Title: Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis.
    Article Snippet: .. Price, R. J. et al. Chromosome-scale genome sequence assemblies of the ‘Autumn Bliss’ and ‘Malling Jewel’ cultivars of the highly heterozygous red raspberry Rubus idaeus L.) derived from long-read Oxford Nanopore sequence data. ..



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    Image Search Results


    A. Example IGV views of a germline and postzygotic mutation in HiFi read data. B. The number of autosomal de novo germline and postzygotic SNVs, insertions and deletions <50 bp, and tandem repeat mutations observed in each sample. Sibling pairs are grouped by family and highlighted in blue, with the proband above the sibling. C. Upset plot of origin assignment shows concordance between HiFi haplotypes, ONT haplotypes, and allele balance. D. Allele balance distribution for autosomal germline and postzygotic SNVs across PacBio HiFi, Illumina, and ONT read data. E. Distribution of the size of autosomal insertions, deletions, and tandem repeat mutations.

    Journal: bioRxiv

    Article Title: Long-read sequencing of trios reveals increased germline and postzygotic mutation rates in repetitive DNA

    doi: 10.1101/2025.07.18.665621

    Figure Lengend Snippet: A. Example IGV views of a germline and postzygotic mutation in HiFi read data. B. The number of autosomal de novo germline and postzygotic SNVs, insertions and deletions <50 bp, and tandem repeat mutations observed in each sample. Sibling pairs are grouped by family and highlighted in blue, with the proband above the sibling. C. Upset plot of origin assignment shows concordance between HiFi haplotypes, ONT haplotypes, and allele balance. D. Allele balance distribution for autosomal germline and postzygotic SNVs across PacBio HiFi, Illumina, and ONT read data. E. Distribution of the size of autosomal insertions, deletions, and tandem repeat mutations.

    Article Snippet: We leveraged long-read Pacific Biosciences high-fidelity (HiFi) sequencing data derived from blood for variant discovery, and both long-read Oxford Nanopore Technologies (ONT) and short-read Illumina data for validation purposes.

    Techniques: Mutagenesis

    Encoding of example deletions by different sequencing methods. Deletion of chr12 121,792,102–121,792,155 could be detected correctly by all sequencing methods ( A ). Deletion of chr5, 114,989,663–114,999,300 could be detected correctly only by long-read sequencing methods ( B ). Values in brackets represent scores predicted by ConsensuSV-ONT, but only for long-read sequencing.

    Journal: Scientific Reports

    Article Title: ConsensuSV-ONT – A modern method for accurate structural variant calling

    doi: 10.1038/s41598-025-01486-1

    Figure Lengend Snippet: Encoding of example deletions by different sequencing methods. Deletion of chr12 121,792,102–121,792,155 could be detected correctly by all sequencing methods ( A ). Deletion of chr5, 114,989,663–114,999,300 could be detected correctly only by long-read sequencing methods ( B ). Values in brackets represent scores predicted by ConsensuSV-ONT, but only for long-read sequencing.

    Article Snippet: The solution is complete in its form and is ready to use not only by computer scientists but accessible and easy to use for everyone working with Oxford Nanopore long-read sequencing data.

    Techniques: Sequencing

    Encoding of merged mutation by different sequencing methods.

    Journal: Scientific Reports

    Article Title: ConsensuSV-ONT – A modern method for accurate structural variant calling

    doi: 10.1038/s41598-025-01486-1

    Figure Lengend Snippet: Encoding of merged mutation by different sequencing methods.

    Article Snippet: The solution is complete in its form and is ready to use not only by computer scientists but accessible and easy to use for everyone working with Oxford Nanopore long-read sequencing data.

    Techniques: Mutagenesis, Sequencing