Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32449 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORF), six novel ORF-containing transcripts, and fifteen transcripts encoding for messages that potentially alter protein functions through truncations or fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Of these, an evolutionary conserved protein was detected containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.
2022-08-30 | PXD034464 | Pride
Project description:Purpose: To generate a reference long-read transcriptomic data set for use in developing new analysis pipelines and comparing their performance with existing methods. Synthetic “sequin” RNA standards (Hardwick et al. 2016) were sequenced using the Oxford Nanopore Technologies (ONT) GridION platform.
2020-06-18 | GSE151984 | GEO
Project description:Apis mellifera genome sequencing and assembly using long-read technologies
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Project description:a chromosome-level nuclear genome and organelle genomes of the alpine snow alga Chloromonas typhlos were sequenced and assembled by integrating short- and long-read sequencing and proteogenomic strategy
2024-10-12 | PXD056928 |
Project description:A new genome of Fraxinus excelsior (PRJNA865134) was assembled using a hybrid approach combining Nanopore and Illumina data. The gene expression of a 182 Danish tree panel (Harper et al. 2016) was assessed using the new genome as reference (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ).Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
2025-03-03 | GSE214551 | GEO
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of T cell functional plasticity as it relates to human health and disease. However, To our knowledge, no long-read transcriptome reference exists for activated human CD4 T cells. To begin to fill this gap, we purified CD4 T cells from the peripheral blood of a healthy female donor and activated these cells with anti-CD3/CD28 beads to generate populations of early activated (4hr), mid-activated (16hr), blasting (48hr) and proliferating (120hr) CD4 T cells. From each of these time points, we obtained high-quality RNA (RIN>9) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis, which we hope will serve as a reference for future transcriptomic studies of these populations. UCSC genome browser tracks for these samples can be accessed at: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=on&position=chr1:206,903,317-206,921,941&hubUrl=http://162.215.210.70/~tracks/Mitchell_IsoSeq_Stim/hub.txt
2025-02-12 | GSE229971 | GEO
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of T cell functional plasticity as it relates to human health and disease. However, To our knowledge, no long-read transcriptome reference exists for activated human CD4 T cells. To begin to fill this gap, we purified CD4 T cells from the peripheral blood of a healthy female donor and activated these cells with anti-CD3/CD28 beads to generate populations of early activated (4hr), mid-activated (16hr), blasting (48hr) and proliferating (120hr) CD4 T cells. From each of these time points, we obtained high-quality RNA (RIN>9) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis, which we hope will serve as a reference for future transcriptomic studies of these populations. UCSC genome browser tracks for these samples can be accessed at: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=on&position=chr1:206,903,317-206,921,941&hubUrl=http://162.215.210.70/~tracks/Mitchell_IsoSeq_Stim/hub.txt
2025-02-12 | GSE229969 | GEO
Project description:Venomous animals have traditionally been studied from a proteomic (but also transcriptomic) perspective, often overlooking the study of venom from a genomic point of view until recently. The rise of genomics has led to an increase in the number of reference genomes for non-model organisms, including venomous taxa, enabling new questions on venom evolution from a genomic context. Although venomous snakes are the fundamental model system in venom research, the number of high-quality reference genomes in the group remains limited. In this study, we present a high-quality chromosome-level reference genome for the Arabian horned viper (Cerastes gasperettii), a highly venomous snake native to the Arabian Peninsula. Our highly-contiguous genome allowed us to explore macrochromosomal rearrangements within the Viperidae family, as well as across squamate reptile evolution. Furthermore, we identified a total of ten different toxins conforming the venom’s core, in line with our proteomic results. We also compared microsyntenic changes in the main toxin gene clusters with those of other venomous snake species, highlighting the pivotal role of gene duplication and loss in the emergence and diversification of the two main toxin families for Cerastes gasperettii. Using Illumina data, we reconstructed the demographic history and genome-wide diversity of the species, revealing how historical aridity likely drove population expansions. Finally, this study highlights the importance of using long-read sequencing as well as chromosome-level reference genomes to disentangle the origin and diversification of toxin families in venomous species.
2025-02-18 | PXD060783 | Pride
Project description:Venomous animals have traditionally been studied from a proteomic (but also transcriptomic) perspective, often overlooking the study of venom from a genomic point of view until recently. The rise of genomics has led to an increase in the number of reference genomes for non-model organisms, including venomous taxa, enabling new questions on venom evolution from a genomic context. Although venomous snakes are the fundamental model system in venom research, the number of high-quality reference genomes in the group remains limited. In this study, we present a high-quality chromosome-level reference genome for the Arabian horned viper (Cerastes gasperettii), a highly venomous snake native to the Arabian Peninsula. Our highly-contiguous genome allowed us to explore macrochromosomal rearrangements within the Viperidae family, as well as across squamate reptile evolution. Furthermore, we identified a total of ten different toxins conforming the venom’s core, in line with our proteomic results. We also compared microsyntenic changes in the main toxin gene clusters with those of other venomous snake species, highlighting the pivotal role of gene duplication and loss in the emergence and diversification of the two main toxin families for Cerastes gasperettii. Using Illumina data, we reconstructed the demographic history and genome-wide diversity of the species, revealing how historical aridity likely drove population expansions. Finally, this study highlights the importance of using long-read sequencing as well as chromosome-level reference genomes to disentangle the origin and diversification of toxin families in venomous species.
2025-02-18 | PXD060777 | Pride
Project description:DNA was extracted from two ash tree samples, one tolerant and one susceptible to ash dieback. The DNA was sequenced using Nanopore technologies and the methylation was called against the new genome (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ) to identify differentially methylated regions between both samples. Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
2025-03-03 | GSE214552 | GEO