Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A hybrid transcriptome assembly reveals coding and non-coding landscapes in Drosophila hemocytes

ABSTRACT: Innate immune responses triggered by Drosophila larval hemocytes have been extensively characterized. However, the full extent of transcriptional and post-transcriptional regulation underlying these processes remains poorly understood. Here, we employed a hybrid sequencing strategy integrating Oxford Nanopore long-read and Illumina short-read sequencing to provide a more comprehensive transcriptome annotation. This enabled discovery of full-length transcripts with novel 5′ and 3′ boundaries and uncovered 349 previously unannotated long non-coding RNAs highly induced during late stages of wasp infestation. To ensure high confidence transcript models, we further eliminated potential intra-priming artifacts specific to long-read cDNA data. This high-confident full-length transcript models helped to reveal cell type–specific lncRNA markers in lamellocytes and crystal cells by single-cell analyses, which recapitulated hemocyte differentiation trajectories. Notably, RNAi-based depletion of two highly induced lncRNAs impaired lamellocyte formation under wasp infestation, highlighting their functional relevance. Collectively, our findings provide detailed insights into the Drosophila larval immune transcriptomes through the long-read sequencing and highlight the regulatory roles of non-coding RNAs in innate immunity.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE329936 | GEO | 2026/05/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Drosophila melanogaster lamellocytes proteome

Project description:In Drosophila melanogaster larval hemolymph, under normal conditions, plasmatocytes and crystal cells represent respectively ~95% and ~5% of hemocytes, while lamellocytes, the third larval cell type, are absent since they are only induced after parasitoid wasp oviposition, their role being the encapsulation-melanization response to eliminate the wasp egg. However, even after induction lamellocytes number remains low, making difficult biochemical studies. Here using the D. melanogaster hopTum-l mutant that constitutively produces a high number of hemocytes, we set up a method to purify lamellocytes and analyzed their major proteins by 2D gel electrophoresis and their biotinylated plasma membrane surface proteins by 1D SDS-PAGE after affinity purification. Mass spectrometry allowed to identify 430 proteins from the 2D spots and 344 from affinity purified proteins, totalizing 639 unique proteins. Known lamellocyte markers such as PPO3 and the integrin myospheroid are among the major proteins and affinity purification led to the detection of other integrins and a large array of integrins associated proteins involved in cell-cell junction formation and function. Overall newly identified proteins indicated that these cells are highly adapted to the encapsulation process but may have also several different physiological functions. This study provides the basis for new lamellocyte studies in vivo and in vitro, and develop markers to search whether different populations coexist, establish their origins and decipher their respective roles in drosophila physiology and immunity.

2024-04-29 | PXD016876 | Pride

Homo sapiens

Project description:FMR1 gene full-length long read sequencing

| PRJNA352714 | ENA

isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

Project description:We report isoCirc, a long-read sequencing strategy coupled with an integrated computational pipeline to characterize full-length circular RNA (circRNA isoforms) using rolling circle amplification (RCA) followed by long-read sequencing. Applying isoCirc to 12 human tissues, we determined full-length structures and examined tissue specificities of circRNA isoforms in human transcriptomes.

2020-09-12 | GSE141693 | GEO

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer

Project description:To identify aberrant splicing isoforms and potential neoantigens, we performed full-length cDNA sequencing of lung adenocarcinoma cell lines using a long-read sequencer MinION. We constructed a comprehensive catalog of aberrant splicing isoforms and detected isoform-specific peptides using proteome analysis.

2020-12-09 | PXD019915 | JPOST Repository

Transcriptome analysis of TSC1 and TSC2 using Nanopore long-read sequencer

Project description:Tuberous sclerosis complex (TSC) is a relatively common autosomal dominant disorder characterized by multiple dysplastic organ lesions and neuropsychiatric symptoms, caused by loss-of-function mutation of either TSC1 or TSC2. Target-capture full-length double-stranded cDNA sequencing using long-read sequencer Nanopore (Nanopore Long-read Target Sequencing) revealed that the various kinds of the TSC1 and TSC2 full-length transcripts and the novel intron retention transcripts of TSC2 in TSC patient. Our results indicate that the Nanopore Long-read Target Sequencing is useful for the detection of mutations and confers information on the full-length alternative splicing transcripts for the genetic diagnosis.

2023-09-04 | GSE241410 | GEO

Single-cell transcriptomics identifies new blood cell populations in Drosophila released at the onset of metamorphosis

Project description:Drosophila blood cells called hemocytes form an efficient barrier against infections and tissue damage. During metamorphosis, hemocytes undergo tremendous changes in their shape and behavior, preparing them for tissue clearance. Yet, the diversity and functional plasticity of pupal blood cells have not been explored. Here, we combine single-cell transcriptomics and high-resolution microscopy to dissect the heterogeneity and plasticity of pupal hemocytes. We identified undifferentiated and specified hemocytes with different molecular signatures associated with distinct functions such as antimicrobial, antifungal immune defense, cell adhesion or secretion. Strikingly, we identified a highly migratory and immuneresponsive pupal cell population expressing typical markers of the posterior signaling center (PSC), which is known to be an important niche in the larval lymph gland. PSC-like cells become restricted to the abdominal segments and are morphologically very distinct from typical Hemolectin (Hml)-positive plasmatocytes. G-TRACE lineage experiments further suggest that PSC-like cells can transdifferentiate to lamellocytes triggered by parasitoid wasp infestation. In summary, we present the first molecular description of pupal Drosophila blood cells, providing insights into blood cell functional diversification and plasticity during pupal metamorphosis.

2023-09-11 | GSE216339 | GEO

A single cell transcriptome atlas of myeloid blood cell lineages in Drosophila [bulk RNA-seq]

Project description:The Drosophila lymph gland (LG) is the larval hematopoietic organ comprised of multipotent prohemocytes and mature hemocytes and has been a valuable model for understanding mechanisms underlying the hematopoiesis and immune responses. There are three types of mature hemocytes in the lymph gland; plasmatocytes, lamellocytes, and crystal cells, all of which are analogous to myeloid-lineage blood cells. To date, the Drosophila hematopoietic system has been primarily defined by classical genetic methods that may limit the promise of its advantage as a model. In this study, we used single-cell RNA sequencing method to comprehensively profile the heterogeneity of developing myeloid hemocytes in the wild-type lymph gland and their transitions upon active immunity caused by wasp infestation. Moreover, we compared hemocytes originated from the embryonic and the lymph gland hematopoiesis and unraveled genetic and cellular diversity of two different ancestries. Finally, hemocytes of the Drosophila lymph gland and human immune cells are contrasted at a transcriptome level, highlighting evolutionary conservations of myeloid cells across species. Overall, our single-cell RNA seq analyses disclose the development of myeloid hemocytes at a single-cell level and provide comparative insights into two different lineages of hemocytes in Drosophila and perspectives on the evolution of myeloid cells, serving as an ample resource for revealing essentials of the hematopoiesis.

2020-07-25 | GSE141274 | GEO

A single cell transcriptome atlas of myeloid blood cell lineages in Drosophila [scRNA-seq]

2020-07-24 | GSE141273 | GEO

Project description:Long-read sequencing to detect full-length protein-protein interactions

| PRJNA1095688 | ENA

Project description:Full-length haplotype reconstruction of CD36 by long-read sequencing

| PRJNA1422979 | ENA