Ontology highlight
ABSTRACT:
PROVIDER: PRJNA805023 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pioneering studies (PXD014844) have identified many interesting molecules in tick saliva by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement the previously released short-read transcriptome-based proteome.
2022-05-31 | PXD033870 | Pride
Project description:Pioneering studies (PXD014844) have identified many interesting molecules by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement previously released short-read transcriptome-based proteome.
2020-01-23 | PXD014844 | Pride
Project description:Phaseolus coccineus Raw sequence reads
| PRJNA415864 | ENA
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:Phaseolus coccineus Transcriptome or Gene expression
| PRJNA79381 | ENA
Project description:Phaseolus coccineus Transcriptome or Gene expression
| PRJNA100195 | ENA
Project description:Phaseolus coccineus Transcriptome or Gene expression
| PRJNA12924 | ENA
Project description:In order to polish a long-read genome assembly, short-read illumina data was obtained from Heterodera schachtii cysts (Woensdrecht population from IRS, the Netherlands). Cysts where obtained from infected plant material. Nematodes were cleaned using a sucrose gradient centrifugation step. Thereafter DNA was extracted and used for library preparation and sequencing by Illumina NextSeq500.
2023-11-03 | E-MTAB-13472 | biostudies-arrayexpress