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22af6328-2143-41a1-902f-3c542ff81c1e - samples

ABSTRACT: MGI standard short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57ÃƒÂ—.

PROVIDER: EGAD00001007044 | EGA |

REPOSITORIES: EGA

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5e179ea6-b04e-455a-839b-4130a61c407c - samples

Project description:MGI CoolMPS short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57ÃƒÂ—.

| EGAD00001007048 | EGA

d3e54fd1-b696-4e3d-8d53-1c93c74c4e76 - samples

Project description:MGI single-tube long fragment read (stLFR) linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~51ÃƒÂ—.

| EGAD00001007045 | EGA

d5495f2a-37a0-4152-8e01-4b2cd239df66 - samples

Project description:Illumina PCR-free sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~44ÃƒÂ—. Sequencing was performed at the Wellcome Centre for Human Genetics on the Illumina Novaseq platform.

| EGAD00001007042 | EGA

Multi-omic profiling of pathogen-stimulated primary immune cells

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

9f28ba52-b3d6-4dbe-8d3a-6985af609115 - samples

Project description:Bionano DLS optical mapping data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a molecule depth of ~153ÃƒÂ—. Optical mapping was performed at the Weatherall Institute of Molecular Medicine using the Bionano Saphyr platform.

| EGAD00001007049 | EGA

Using de novo assembly to identify structural variation of complex immune system gene regions

Project description:Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity. Several factors contribute to this including inheritable structural polymorphism of the underlying genes. To investigate this we generated data for a single healthy European individual (identified as HV31) using multiple long-read (PacBio Sequel II and Oxford Nanopore), short-read (Illumina HiSeq and MGI G400) and linked-read (10X Chromium and stLFR) sequencing platforms, and optical mapping using the Bionano Saphyr platform. DNA was extracted from monocytes or from peripheral blood mononuclear cells. We used these data to assemble a set of regions encoding components of the immune system and to investigate structural variation. The raw data and analysis results are deposited here for generate research use. A complete description of these data and results can be found in the accompanying article at https://doi.org/10.1101/2021.02.03.429586.

| EGAS00001005046 | EGA

be0d489f-6483-4d9f-a9cb-4addd1a7a9aa - samples

Project description:PacBio continuous long read (CLR) sequencing data for individual HV31 generated on PacBio Sequel II instrument, using DNA from CD14+ monocytes, to a sequencing depth of ~35ÃƒÂ—. Sequencing was performed at the Wellcome Sanger Institute.

| EGAD00001007047 | EGA

LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [Loop QC]

Project description:In this study, we used a barcoding-based synthetic long read (SLR) isoform sequencing approach (LoopSeq) to generate sequencing reads sufficiently long and accurate to identify isoforms using standard short read Illumina sequencers.

2021-05-05 | GSE155920 | GEO

LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [RNA-seq]

2021-05-05 | GSE155375 | GEO

High-throughput error corrected Nanopore single cell transcriptome sequencing

Project description:E18 mouse brain single cell profiling using the 10x Genomics Chromium instrument workflow with either Illumina short read sequencing for the standard gene profiling and Nanopore PromethION long read sequencing for isoform profiling.

2020-07-10 | GSE130708 | GEO

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