Ontology highlight
ABSTRACT:
PROVIDER: PRJNA885118 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Objectives: To perform long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors. We aim to discover new transcripts and protein isoforms expressed during immune responses to diverse pathogens. Methods: PBMCs were exposed to four microbial stimuli for 24 hours: the TLR4 ligand lipopolysaccharide (LPS), the TLR3 ligand Poly(I:C), heat-inactivated Staphylococcus aureus, Candida albicans, and RPMI medium as negative controls. Long-read sequencing (PacBio) of one donor and secretome proteomics and short-read sequencing of five donors were performed. IsoQuant was used for transcriptome construction, Metamorpheus/FlashLFQ for proteome analysis, and Illumina short-read 3’-end mRNA sequencing for transcript quantification. Results: Long-read transcriptome profiling reveals the expression of novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. We observe widespread loss of intron retention as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. In general, RNA expression differences did not result in differences in the amounts of secreted proteins. Interindividual differences in the proteome were larger than the differences between stimulated and unstimulated PBMCs. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and Poly(I:C)-stimulated PBMCs. Conclusion: Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.
2023-09-16 | PXD045237 | Pride
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:Provide a comprehensive picture of HERV RNA expression through both short and long read sequencing in NCCIT cells to be used in an integrated proteogenomic analysis pipeline
2025-01-08 | PXD054413 | Pride
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE246836 | GEO
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE246835 | GEO
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE246832 | GEO
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE246830 | GEO
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE269801 | GEO
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE269800 | GEO